QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  

   Search term(s): Transcription

GO Term Name(GO Accession Number)Term TypeDefinition
regulation of transcription involved in G1/S transition of mitotic cell cycle(GO:0000083)biological_processAny process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
obsolete regulation of transcription involved in G1 phase of mitotic cell cycle(GO:0000114)biological_processOBSOLETE. Any process that regulates transcription such that the target genes are transcribed as part of the G1 phase of the mitotic cell cycle. This term was made obsolete because it is unclear exactly what it means. It could mean either 'regulation of transcription during phase X' or 'regulation of transition between phase X and phase Y'.
obsolete regulation of transcription involved in S phase of mitotic cell cycle(GO:0000115)biological_processOBSOLETE. A cell cycle process that regulates transcription such that the target genes are transcribed as part of the S phase of the mitotic cell cycle. This term was made obsolete because it is unclear exactly what it means. It could mean either 'regulation of transcription during phase X' or 'regulation of transition between phase X and phase Y'.
obsolete regulation of transcription involved in G2-phase of mitotic cell cycle(GO:0000116)biological_processOBSOLETE. Any process that regulates transcription such that the target genes are transcribed as part of the G2 phase of the mitotic cell cycle. This term was made obsolete because it is unclear exactly what it means. It could mean either 'regulation of transcription during phase X' or 'regulation of transition between phase X and phase Y'.
regulation of transcription involved in G2/M transition of mitotic cell cycle(GO:0000117)biological_processAny process that regulates transcription such that the target genes are transcribed as part of the G2/M transition of the mitotic cell cycle.
RNA polymerase I transcription factor complex(GO:0000120)cellular_componentA transcription factor complex that acts at a regulatory region of a gene transcribed by RNA polymerase I.
negative regulation of transcription by RNA polymerase II(GO:0000122)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
transcription factor TFIIIB complex(GO:0000126)cellular_componentA transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIB contains the TATA-binding protein (TBP) and two Pol III-specific proteins, B'' and BRF.
transcription factor TFIIIC complex(GO:0000127)cellular_componentA heterotrimeric transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIC contains three conserved subunits that associate with the proximal Pol III promoter element, and additional subunits that associate with sequence elements downstream of the promoter and are more diverged among species. It also functions as a boundary element to partition genome content into distinct domains outside Pol III promoter regions.
transcription export complex(GO:0000346)cellular_componentThe transcription export (TREX) complex couples transcription elongation by RNA polymerase II to mRNA export. The complex associates with the polymerase and travels with it along the length of the transcribed gene. TREX is composed of the THO transcription elongation complex as well as other proteins that couple THO to mRNA export proteins. The TREX complex is known to be found in a wide range of eukaryotes, including S. cerevisiae and metazoans.
regulation of transcription by galactose(GO:0000409)biological_processAny process involving galactose that modulates the frequency, rate or extent or transcription.
carbon catabolite repression of transcription by galactose(GO:0000410)biological_processA transcription regulation process in which the presence of galactose that leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances.
positive regulation of transcription by galactose(GO:0000411)biological_processAny process involving galactose that activates or increases the rate of transcription.
carbon catabolite regulation of transcription from RNA polymerase II promoter(GO:0000429)biological_processA transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources.
regulation of transcription from RNA polymerase II promoter by glucose(GO:0000430)biological_processAny process involving glucose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of transcription from RNA polymerase II promoter by galactose(GO:0000431)biological_processAny process involving galactose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of transcription from RNA polymerase II promoter by glucose(GO:0000432)biological_processAny process involving glucose that activates or increases the rate of transcription from an RNA polymerase II promoter.
carbon catabolite repression of transcription from RNA polymerase II promoter by glucose(GO:0000433)biological_processA transcription regulation process in which the presence of glucose leads to a decrease in the frequency, rate, or extent of transcription of specific RNA polymerase II-transcribed genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances.
carbon catabolite repression of transcription from RNA polymerase II promoter by galactose(GO:0000434)biological_processAny process involving galactose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
positive regulation of transcription from RNA polymerase II promoter by galactose(GO:0000435)biological_processAny process involving galactose that activates or increases the rate of transcription from an RNA polymerase II promoter.
carbon catabolite activation of transcription from RNA polymerase II promoter(GO:0000436)biological_processAny process involving carbon catabolites that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
carbon catabolite repression of transcription from RNA polymerase II promoter(GO:0000437)biological_processA transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources.
transcription factor TFIIH core complex(GO:0000439)cellular_componentThe 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD.
THO complex part of transcription export complex(GO:0000445)cellular_componentThe THO complex when it is part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1, Tho2, Thp1, and Mft1, while the human complex is composed of 7 subunits.
transcription-coupled nucleotide-excision repair, DNA damage recognition(GO:0000716)biological_processThe identification of lesions on the actively transcribed strand of the DNA duplex as well as a small subset of lesions not recognized by the general nucleotide-excision repair pathway.
transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery(GO:0000972)biological_processThe chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery. In S. cerevisiae, this process involves cis-acting DNA sequences such as the TATA box and upstream activating sequence (UAS) elements, trans-acting transcriptional activators, and also the 3'-UTR of the transcript.
posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery(GO:0000973)biological_processThe chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery even after transcription has been repressed.
transcription regulatory region sequence-specific DNA binding(GO:0000976)molecular_functionInteracting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
DNA-binding transcription factor activity, RNA polymerase II-specific(GO:0000981)molecular_functionA protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
transcription factor activity, RNA polymerase II proximal promoter sequence-specific DNA binding(GO:0000982)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
transcription factor activity, RNA polymerase II core promoter sequence-specific DNA binding(GO:0000983)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to modulate transcription by Pol II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
obsolete transcription factor activity, protein binding(GO:0000988)molecular_functionOBSOLETE. Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent. For more details see https://github.com/geneontology/go-ontology/issues/16053
transcription regulator activity(GO:0140110)molecular_functionA molecular function that controls the rate, timing and/or magnitude of transcription of genetic information. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism.
obsolete transcription factor activity, transcription factor binding(GO:0000989)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent. For more details see https://github.com/geneontology/go-ontology/issues/16053
transcription factor binding(GO:0008134)molecular_functionInteracting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
obsolete transcription factor activity, core RNA polymerase binding(GO:0000990)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent. For more details see https://github.com/geneontology/go-ontology/issues/16053
obsolete transcription factor activity, core RNA polymerase II binding(GO:0000991)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent. For more details see https://github.com/geneontology/go-ontology/issues/16053
RNA polymerase III general transcription initiation factor activity(GO:0000995)molecular_functionAn activity that contributes to transcription start site selection and transcription initiation of genes transcribed by RNA polymerase III. Factors required for RNA polymerase III transcription initiation include TFIIIA, TFIIIB and TFIIIC.
RNA polymerase III transcription regulator recruiting activity(GO:0001004)molecular_functionInitiating the assembly of the RNA polymerase III pre-initiation complex by binding to a control sequence in the intragenic region. This allows to recruit TFIIIB to the DNA at a site centered approximately 26 base pairs upstream of the start site of transcription. For tRNA genes, TFIIIC first associates with DNA, and then recruits TFIIIB. For 5S rRNA genes, TFIIIA binds to DNA first, followed by TFIIIC, which then recruits TFIIIB.
obsolete transcription factor activity, RNA polymerase III transcription factor binding(GO:0001007)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity(GO:0001010)molecular_functionThe function of binding to a specific DNA sequence and recruiting another transcription factor to the DNA in order to modulate transcription. The recruited factor may bind DNA directly, or may be colocalized via protein-protein interactions.
transcription factor activity, sequence-specific DNA binding, RNA polymerase recruiting(GO:0001011)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence and recruiting RNA polymerase to the DNA in order to form the preinitiation complex (PIC).
snoRNA transcription by RNA polymerase III(GO:0001014)biological_processThe synthesis of small nucleolar RNA (snoRNA) from a DNA template by RNA polymerase III, originating at a type 2 RNA polymerase III promoter.
snoRNA transcription by RNA polymerase II(GO:0001015)biological_processThe synthesis of small nucleolar RNA (snoRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.
RNA polymerase III transcription factor binding(GO:0001025)molecular_functionInteracting selectively and non-covalently with an RNA polymerase III transcription factor, any protein required to initiate or regulate transcription by RNA polymerase III.
obsolete TFIIIB-type transcription factor activity(GO:0001026)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, Once recruited to an RNA polymerase III promoter by one or more other transcription factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex. This term was obsoleted because it represents a gene product.
obsolete RNA polymerase III type 1 promoter TFIIIB-type transcription factor activity(GO:0001027)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 1 promoter by TFIIIA-type and TFIIIC-type factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex. The reason for obsoletion is that there is a single TFIIIB activity; this is not dependent on the promoter.
obsolete RNA polymerase III type 2 promoter TFIIIB-type transcription factor activity(GO:0001028)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 2 promoter by a TFIIIC-type factor, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex. The reason for obsoletion is that there is a single TFIIIB activity; this is not dependent on the promoter.
obsolete RNA polymerase III type 3 promoter TFIIIB-type transcription factor activity(GO:0001029)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 3 promoter by SNAP-type and TFIIIC-type factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex.
obsolete RNA polymerase III hybrid type promoter TFIIIB-type transcription factor activity(GO:0001040)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III hybrid type promoter, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex. The reason for obsoletion is that there is a single TFIIIB activity; this is not dependent on the promoter.
transcription by RNA polymerase IV(GO:0001059)biological_processThe synthesis of RNA from a DNA template by RNA polymerase IV (Pol III), originating at a Pol IV-specific promoter.
transcription by RNA polymerase V(GO:0001060)biological_processThe synthesis of RNA from a DNA template by RNA polymerase V (Pol III), originating at a Pol V-specific promoter.
transcription regulatory region RNA binding(GO:0001068)molecular_functionInteracting selectively and non-covalently with a RNA region within the transcript that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon.
RNA-binding transcription regulator activity(GO:0001070)molecular_functionInteracting selectively and non-covalently with an RNA sequence in order to modulate transcription. This function is known to occur in phages and viruses, for example the lambda N and the HIV tat proteins are necessary to allow RNA polymerase to read through terminator sequences.
transcription antitermination factor activity, RNA binding(GO:0001072)molecular_functionBinds to RNA, typically within the nascent RNA transcript, to promote readthrough of a transcription termination site and thus extending the length of the RNA transcript produced. Examples of antitermination factors which bind the nascent RNA include the lambda N protein and the HIV-1 tat protein.
transcription antitermination factor activity, DNA binding(GO:0001073)molecular_functionBinds to DNA, typically within region of the promoter and transcribed region, to promote readthrough of a transcription termination site and thus extending the length of the RNA transcript produced. Examples of antitermination factors which bind DNA include the lambda Q protein.
transcription factor activity, RNA polymerase II proximal promoter sequence-specific DNA binding involved in preinitiation complex assembly(GO:0001074)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter.
transcription factor activity, RNA polymerase II core promoter sequence-specific binding involved in preinitiation complex assembly(GO:0001075)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter.
obsolete transcription factor activity, RNA polymerase II transcription factor binding(GO:0001076)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent. For more details see https://github.com/geneontology/go-ontology/issues/16053
RNA polymerase II transcription factor binding(GO:0001085)molecular_functionInteracting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific(GO:0001077)molecular_functionA protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within a proximal promoter regulatory region of a RNA polymerase II-transcribed gene to activate or increase transcription.
proximal promoter DNA-binding transcription repressor activity, RNA polymerase II-specific(GO:0001078)molecular_functionA protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within a proximal promoter regulatory region of a RNA polymerase II-transcribed gene to repress or decrease transcription.
nitrogen catabolite regulation of transcription from RNA polymerase II promoter(GO:0001079)biological_processA transcription regulation process in which the presence of one nitrogen source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
nitrogen catabolite activation of transcription from RNA polymerase II promoter(GO:0001080)biological_processA transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
nitrogen catabolite repression of transcription from RNA polymerase II promoter(GO:0001081)biological_processA transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
obsolete transcription factor activity, RNA polymerase I transcription factor binding(GO:0001082)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase I transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
obsolete transcription factor activity, RNA polymerase II basal transcription factor binding(GO:0001083)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
obsolete transcription factor activity, TFIID-class binding(GO:0001084)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
TFIID-class transcription factor complex binding(GO:0001094)molecular_functionInteracting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIID complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
obsolete transcription factor activity, TFIIA-class binding(GO:0001086)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIA class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
TFIIA-class transcription factor complex binding(GO:0001092)molecular_functionInteracting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIIA complex, one of the complexes involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
obsolete transcription factor activity, TFIIB-class binding(GO:0001087)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIB class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
TFIIB-class transcription factor binding(GO:0001093)molecular_functionInteracting selectively and non-covalently with a general RNA polymerase II transcription factor of the TFIIB class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
obsolete transcription factor activity, TFIIE-class binding(GO:0001088)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIE class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
TFIIE-class transcription factor complex binding(GO:0001095)molecular_functionInteracting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIIE complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
obsolete transcription factor activity, TFIIF-class transcription factor binding(GO:0001089)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIF class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
TFIIF-class transcription factor complex binding(GO:0001096)molecular_functionInteracting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIIF complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
obsolete transcription factor activity, TFIIH-class binding(GO:0001090)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIH class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
RNA polymerase II basal transcription factor binding(GO:0001091)molecular_functionInteracting selectively and non-covalently with a basal RNA polymerase II transcription factor, any of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
TFIIH-class transcription factor complex binding(GO:0001097)molecular_functionInteracting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIIH complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
basal transcription machinery binding(GO:0001098)molecular_functionInteracting selectively and non-covalently with the basal transcription machinery which is composed of the RNA polymerase core enzyme and the basal transcription factor(s), the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase.
basal RNA polymerase II transcription machinery binding(GO:0001099)molecular_functionInteracting selectively and non-covalently with the basal transcription machinery for RNA polymerase II which is composed of the RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits, and the basal RNA polymerase II transcription factors, the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase.
RNA polymerase II activating transcription factor binding(GO:0001102)molecular_functionInteracting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
RNA polymerase II repressing transcription factor binding(GO:0001103)molecular_functionInteracting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription.
promoter clearance during DNA-templated transcription(GO:0001109)biological_processAny process involved in the transition from the initiation to the elongation phases of transcription by a DNA-dependent RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors.
DNA-templated transcriptional open complex formation(GO:0001112)biological_processAny process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble.
transcriptional open complex formation at RNA polymerase II promoter(GO:0001113)biological_processAny process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble.
transcription ternary complex disassembly(GO:0001118)biological_processThe disaggregation of a transcription ternary complex, composed of RNA polymerase, template DNA, and an RNA transcript, into its constituent components.
bacterial transcription(GO:0001121)biological_processThe synthesis of RNA from a DNA template by a bacterial-type RNA polymerase, originating at a bacterial-type promoter.
transcription initiation from bacterial-type RNA polymerase promoter(GO:0001123)biological_processAny process involved in the assembly of bacterial-type RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
transcription elongation from bacterial-type RNA polymerase promoter(GO:0001124)biological_processThe extension of an RNA molecule after transcription initiation and promoter clearance at a bacterial-type RNA polymerase promoter by the addition of ribonucleotides catalyzed by a bacterial-type RNA polymerase.
transcription termination from bacterial-type RNA polymerase promoter(GO:0001125)biological_processThe process in which the synthesis of an RNA molecule by a bacterial-type RNA polymerase using a DNA template is completed.
transcriptional open complex formation at bacterial-type RNA polymerase promoter(GO:0001127)biological_processAny process involved in the melting of the DNA hybrid of the core promoter region within a bacterial-type RNA polymerase promoter to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble.
RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly(GO:0001128)molecular_functionInteracting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or stability of the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC). Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
obsolete RNA polymerase II transcription factor activity, TBP-class protein binding, involved in preinitiation complex assembly(GO:0001129)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), to facilitate the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase. The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent. For more details see https://github.com/geneontology/go-ontology/issues/16053
bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding(GO:0001130)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
transcription factor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding(GO:0001131)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
obsolete RNA polymerase II transcription factor activity, TBP-class protein binding(GO:0001132)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well. The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent. For more details see https://github.com/geneontology/go-ontology/issues/16053
transcription regulator recruiting activity(GO:0001134)molecular_functionThe function of binding to an RNA polymerase (RNAP) transcription regulator and recruiting it to the general transcription machinery complex in order to modulate transcription initiation.
RNA polymerase II transcription regulator recruiting activity(GO:0001135)molecular_functionThe function of binding to an RNA polymerase II (RNAP II) transcription regulator and recruiting it to the general transcription machinery complex in order to modulate transcription initiation.
transcriptional activator activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding(GO:0001140)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to increase transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
transcriptional repressor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding(GO:0001141)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to stop, prevent, or reduce the frequency, rate or extent of transcription from a bacterial-type RNA polymerase promoter.
transcription termination site sequence-specific DNA binding(GO:0001147)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon.
transcription factor activity, bacterial-type RNA polymerase termination site sequence-specific binding(GO:0001149)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is a termination site for bacterial-type RNA polymerase in order to promote transcription termination by bacterial-type RNA polymerase.
transcription factor activity, bacterial-type RNA polymerase transcription enhancer sequence-specific binding(GO:0001151)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is a bacterial-type enhancer region in order to activate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. Enhancers for sigma-54 holoenzymes are typically located 80 to 150 base pairs upstream from the transcription start site. Some transcription units dependent on sigma-70 holoenzymes may also include enhancer sequences.
obsolete transcription factor activity, RNA polymerase III type 1 promoter sequence-specific binding, TFIIIC recruiting(GO:0001152)molecular_functionOBSOLETE. The function of binding to a specific DNA sequence motif in a type 1 RNA polymerase III (Pol III) promoter in order to recruit the transcription factor TFIIIC to the promoter. This term was made obsolete in the 2018 Transcription branch revision. This represents the activity of TFIIIA only.
obsolete transcription factor activity, RNA polymerase III transcription factor recruiting(GO:0001153)molecular_functionOBSOLETE. The function of binding to an RNA polymerase III (RNAP III) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP III. This term was made obsolete in the 2018 Transcription branch revision. This term was redundant with other terms.
TFIIIB-class transcription factor complex binding(GO:0001154)molecular_functionInteracting selectively and non-covalently with a general RNA polymerase III transcription factor belonging to the TFIIB complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III.
TFIIIA-class transcription factor binding(GO:0001155)molecular_functionInteracting selectively and non-covalently with an RNA polymerase III transcription factor of the TFIIIA class, one of the factors involved in formation of the preinitiation complex (PIC) at RNA polymerase III promoters.
TFIIIC-class transcription factor complex binding(GO:0001156)molecular_functionInteracting selectively and non-covalently with a general RNA polymerase III transcription factor belonging to the TFIIC complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III.
transcription termination site DNA binding(GO:0001160)molecular_functionInteracting selectively and non-covalently with a region of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon.
intronic transcription regulatory region sequence-specific DNA binding(GO:0001161)molecular_functionInteracting selectively and non-covalently with an intronic DNA sequence that regulates the transcription of the transcript it is contained within.
RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding(GO:0001162)molecular_functionInteracting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within.
obsolete RNA polymerase I transcription factor activity, sequence-specific DNA binding(GO:0001167)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase I. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child. See https://github.com/geneontology/go-ontology/issues/15787.
obsolete transcription factor activity, RNA polymerase I upstream control element sequence-specific binding(GO:0001168)molecular_functionOBSOLETE. Interacting selectively and non-covalently with the upstream control element (UCE, or alternately referred to as the upstream element, UE), a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase I in order to modulate transcription by RNA polymerase I. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child. See https://github.com/geneontology/go-ontology/issues/15787.
obsolete transcription factor activity, RNA polymerase I CORE element sequence-specific binding(GO:0001169)molecular_functionOBSOLETE. Interacting selectively and non-covalently with CORE element, a regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery in order to modulate transcription by RNA polymerase I. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child. See https://github.com/geneontology/go-ontology/issues/15787.
obsolete transcription factor activity, RNA polymerase I enhancer sequence-specific binding(GO:0001170)molecular_functionOBSOLETE. Interacting selectively and non-covalently with a RNA polymerase I (Pol I) enhancer in order to modulate transcription by RNA polymerase I. This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child. See https://github.com/geneontology/go-ontology/issues/15787.
reverse transcription(GO:0001171)biological_processA DNA synthesis process that uses RNA as the initial template for synthesis of DNA, but which also includes an RNase activity to remove the RNA strand of an RNA-DNA heteroduplex produced by the RNA-dependent synthesis step and use of the initial DNA strand as a template for DNA synthesis.
transcription, RNA-templated(GO:0001172)biological_processThe cellular synthesis of RNA on a template of RNA.
DNA-templated transcriptional start site selection(GO:0001173)biological_processAny process involved in the selection of the specific location within the template strand of a DNA-dependent RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
transcriptional start site selection at RNA polymerase II promoter(GO:0001174)biological_processAny process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
transcriptional start site selection at RNA polymerase III promoter(GO:0001175)biological_processAny process involved in the selection of the specific location within the template strand of an RNA polymerase III promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
transcriptional start site selection at bacterial-type RNA polymerase promoter(GO:0001176)biological_processAny process involved in the selection of the specific location within the template strand of a bacterial-type RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
regulation of transcriptional open complex formation at RNA polymerase II promoter(GO:0001177)biological_processAny process that modulates the rate, frequency or extent of a process involved the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble.
regulation of transcriptional start site selection at RNA polymerase II promoter(GO:0001178)biological_processAny process that modulates the rate, frequency or extent of a process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
RNA polymerase I transcription factor binding(GO:0001179)molecular_functionInteracting selectively and non-covalently with an RNA polymerase I transcription factor, any protein required to initiate or regulate transcription by RNA polymerase I.
RNA polymerase I general transcription initiation factor activity(GO:0001181)molecular_functionAn activity that contributes to transcription start site selection and transcription initiation of genes transcribed by RNA polymerase I. Factors required for RNA polymerase I transcription initiation include upstream activation factor (UAF), core factor (CF), TATA binding protein (TBP) and RRN3.
transcription elongation from RNA polymerase I promoter for nuclear large rRNA transcript(GO:0001183)biological_processThe extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I promoter for the nuclear large ribosomal RNA (rRNA) transcript by the addition of ribonucleotides catalyzed by RNA polymerase I.
RNA polymerase I transcription regulator recruiting activity(GO:0001186)molecular_functionThe function of binding to an RNA polymerase I (RNAP I) transcription regulator and recruiting it to the general transcription machinery complex in order to modulate transcription initiation.
obsolete transcriptional activator activity, RNA polymerase II transcription factor binding(GO:0001190)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent. For more details see https://github.com/geneontology/go-ontology/issues/16053
DNA-binding transcription activator activity, RNA polymerase II-specific(GO:0001228)molecular_functionA protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to activate or increase transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
obsolete transcriptional repressor activity, RNA polymerase II transcription factor binding(GO:0001191)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well. The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent. For more details see https://github.com/geneontology/go-ontology/issues/16053
DNA-binding transcription repressor activity, RNA polymerase II-specific(GO:0001227)molecular_functionA protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to repress or decrease transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
maintenance of transcriptional fidelity during DNA-templated transcription elongation(GO:0001192)biological_processSuppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation on a DNA template.
maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter(GO:0001193)biological_processSuppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from an RNA polymerase II promoter.
maintenance of transcriptional fidelity during DNA-templated transcription elongation from bacterial-type RNA polymerase promoter(GO:0001194)biological_processSuppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from a bacterial-type RNA polymerase promoter.
maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase III promoter(GO:0001195)biological_processSuppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from a RNA polymerase III promoter.
regulation of mating-type specific transcription from RNA polymerase II promoter(GO:0001196)biological_processAny mating-type specific process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of mating-type specific transcription from RNA polymerase II promoter(GO:0001197)biological_processAny mating-type specific process that activates or increases the rate of transcription from an RNA polymerase II promoter.
negative regulation of mating-type specific transcription from RNA polymerase II promoter(GO:0001198)biological_processAny mating-type specific process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
transcription factor activity, metal ion regulated sequence-specific DNA binding(GO:0001199)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to modulate transcription by an RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist.
RNA polymerase II transcription factor activity, metal ion regulated sequence-specific DNA binding(GO:0001200)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to modulate transcription by RNA polymerase II. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist.
RNA polymerase II transcription factor activity, metal ion regulated proximal promoter sequence-specific DNA binding(GO:0001201)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor that binds the core promoter proximal region in order to modulate transcription by RNA polymerase II. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist.
RNA polymerase II transcription factor activity, copper ion regulated proximal promoter sequence-specific DNA binding(GO:0001202)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with copper(I) (Cu+) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+), such a way that copper ion binding regulates the activity of the transcription factor, perhaps by regulating the ability to interact selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II), or by regulating some other function of the transcription factor, in order to modulate transcription by RNAP II.
RNA polymerase II transcription factor activity, zinc ion regulated proximal promoter sequence-specific DNA binding(GO:0001203)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with zinc (Zn) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of zinc (Zn), in such a way that zinc ion binding regulates the activity of the transcription factor, perhaps by regulating the ability to interact selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II), or by regulating some other function of the transcription factor, in order to modulate transcription by RNAP II.
bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding(GO:0001204)molecular_functionInteracting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to modulate transcription by a bacterial-type RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist.
distal enhancer DNA-binding transcription activator activity, RNA polymerase II-specific(GO:0001205)molecular_functionA protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the distal enhancer regulatory region of a RNA polymerase II-transcribed gene to activate or increase transcription.
distal enhancer DNA-binding transcription repressor activity, RNA polymerase II-specific(GO:0001206)molecular_functionA protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the distal enhancer regulatory region of a RNA polymerase II-transcribed gene to repress or decrease transcription from a RNA polymerase II promoter.
transcriptional activator activity, metal ion regulated sequence-specific DNA binding(GO:0001209)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of cellular DNA-dependent transcription by an RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist.
transcriptional repressor activity, metal ion regulated sequence-specific DNA binding(GO:0001210)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by an RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist.
RNA polymerase II transcriptional activator activity, copper ion regulated proximal promoter sequence-specific DNA binding(GO:0001211)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with copper(I) (Cu+) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+), such a way that copper ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
RNA polymerase II transcriptional activator activity, zinc ion regulated proximal promoter sequence-specific DNA binding(GO:0001212)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with zinc (Zn) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of zinc (Zn), such a way that copper ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
RNA polymerase II transcriptional activator activity, metal ion regulated proximal promoter sequence-specific DNA binding(GO:0001213)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of metal ion, such a way that metal ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
RNA polymerase II transcriptional repressor activity, metal ion regulated proximal promoter sequence-specific DNA binding(GO:0001214)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of metal ion, such a way that metal ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
bacterial-type RNA polymerase transcriptional activator activity, metal ion regulated sequence-specific DNA binding(GO:0001215)molecular_functionInteracting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist.
bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding(GO:0001216)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence in order to activate or increase the frequency, rate or extent of transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
bacterial-type RNA polymerase transcriptional repressor activity, sequence-specific DNA binding(GO:0001217)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence in order to stop, prevent, or reduce the frequency, rate or extent of transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
bacterial-type RNA polymerase transcriptional repressor activity, metal ion regulated sequence-specific DNA binding(GO:0001218)molecular_functionInteracting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist.
bacterial-type RNA polymerase transcriptional repressor activity, copper ion regulated sequence-specific DNA binding(GO:0001219)molecular_functionInteracting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with copper(I) (Cu+) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+), in such a way that copper ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase.
bacterial-type RNA polymerase transcriptional repressor activity, cadmium ion regulated sequence-specific DNA binding(GO:0001220)molecular_functionInteracting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with cadmium (Cd) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of cadmium (Cd), in such a way that cadmium (Cd) ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase.
transcription cofactor binding(GO:0001221)molecular_functionInteracting selectively and non-covalently with a transcription cofactor, any protein involved in regulation of transcription via protein-protein interactions with transcription factors and other transcription regulatory proteins. Cofactors do not bind DNA directly, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
transcription corepressor binding(GO:0001222)molecular_functionInteracting selectively and non-covalently with a transcription corepressor, any protein involved in negative regulation of transcription via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery.
transcription coactivator binding(GO:0001223)molecular_functionInteracting selectively and non-covalently with a transcription coactivator, any protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
RNA polymerase II transcription cofactor binding(GO:0001224)molecular_functionInteracting selectively and non-covalently with a transcription cofactor for RNA polymerase II, any protein involved in regulation of transcription via protein-protein interactions with RNA polymerase II transcription factors and other transcription regulatory proteins. Cofactors do not bind DNA directly, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery of RNA polymerase II.
RNA polymerase II transcription coactivator binding(GO:0001225)molecular_functionInteracting selectively and non-covalently with an RNA polymerase II transcription coactivator, any protein involved in positive regulation of transcription of RNA polymerase II via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery of RNA polymerase II.
RNA polymerase II transcription corepressor binding(GO:0001226)molecular_functionInteracting selectively and non-covalently with an RNA polymerase II transcription corepressor, any protein involved in negative regulation of transcription by RNA polymerase II via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery of RNA polymerase II.
cotranscriptional mitochondrial rRNA nucleotide insertion(GO:0002110)biological_processThe insertion of one or two non-coded nucleotides during the transcription of a mitochondrial rRNA. Such additions are known to occur in myxomycetes such as Physarum, Didymium, and Stemonitis.
regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation(GO:0003256)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of a myocardial precursor cell.
positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation(GO:0003257)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of a myocardial precursor cell.
regulation of transcription from RNA polymerase II promoter involved in endocardial precursor cell differentiation(GO:0003258)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of an endocardial precursor cell.
DNA-binding transcription factor activity(GO:0003700)molecular_functionA protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
obsolete RNA polymerase I transcription factor activity(GO:0003701)molecular_functionOBSOLETE. Functions to initiate or regulate RNA polymerase I transcription. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
transcription by RNA polymerase I(GO:0006360)biological_processThe synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.
obsolete RNA polymerase II transcription factor activity(GO:0003702)molecular_functionOBSOLETE. Functions to initiate or regulate RNA polymerase II transcription. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
transcription by RNA polymerase II(GO:0006366)biological_processThe synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
obsolete specific RNA polymerase II transcription factor activity(GO:0003704)molecular_functionOBSOLETE. Functions to enable the transcription of specific, or specific sets, of genes by RNA polymerase II. This term was obsoleted because "general/nonspecific/basal" transcription vs "specific" transcription were determined not to be separable, distinct process. Thus, terms trying to distinguish "general/nonspecific/basal" transcription from "specific" transcription were removed from both the Molecular Function and the Biological Process ontologies. In addition, this Molecular Function term was defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding(GO:0003705)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
obsolete ligand-regulated transcription factor activity(GO:0003706)molecular_functionOBSOLETE. Functions to enable the transcription of specific, or specific sets, of genes by RNA polymerase II in response to a ligand. This term was made obsolete because it does not convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism.
obsolete RNA polymerase III transcription factor activity(GO:0003709)molecular_functionOBSOLETE. Functions to initiate or regulate RNA polymerase III transcription. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
transcription by RNA polymerase III(GO:0006383)biological_processThe synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.
transcription elongation regulator activity(GO:0003711)molecular_functionA molecular function that regulates transcriptional elongation by enabling the transition from transcription initiation to elongation or by altering the elongation properties of the enzyme during the elongation phase of transcription.
transcription coregulator activity(GO:0003712)molecular_functionA protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to either activate or repress the transcription of specific genes. Coregulators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. A third class modulates interactions of DNA-binding transcription factor with other transcription coregulators.
transcription coactivator activity(GO:0003713)molecular_functionA protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to activate the transcription of specific genes. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. Another type of coregulator activity is the bridging of a DNA-binding transcription factor to the basal transcription machinery. The Mediator complex, which bridges transcription factors and RNA polymerase, is also a transcription coactivator.
transcription corepressor activity(GO:0003714)molecular_functionA protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to repress the transcription of specific genes. Corepressors often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. A third class occludes DNA-binding transcription factor protein-protein interaction domains. A third class of corepressors prevents interactions of DNA bound DNA-binding transcription factor with coactivators.
obsolete transcription termination factor activity(GO:0003715)molecular_functionOBSOLETE. Any activity that brings about termination of transcription. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
DNA-templated transcription, termination(GO:0006353)biological_processThe cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
obsolete RNA polymerase I transcription termination factor activity(GO:0003716)molecular_functionOBSOLETE. Any activity that brings about termination of transcription by RNA polymerase I. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
termination of RNA polymerase I transcription(GO:0006363)biological_processThe process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit.
obsolete RNA polymerase II transcription termination factor activity(GO:0003717)molecular_functionOBSOLETE. Any activity that brings about termination of transcription by RNA polymerase II. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
termination of RNA polymerase II transcription(GO:0006369)biological_processThe process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
obsolete RNA polymerase III transcription termination factor activity(GO:0003718)molecular_functionOBSOLETE. Any activity that brings about termination of transcription by RNA polymerase III. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
termination of RNA polymerase III transcription(GO:0006386)biological_processThe process in which transcription by RNA polymerase III is terminated; Pol III has an intrinsic ability to terminate transcription upon incorporation of 4 to 6 contiguous U residues.
obsolete transcription factor binding, cytoplasmic sequestering(GO:0003719)molecular_functionOBSOLETE (was not defined before being made obsolete). This term was made obsolete because sequestering is a process rather than a function.
cytoplasmic sequestering of transcription factor(GO:0042994)biological_processThe selective interaction of a transcription factor with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus.
transcription factor complex(GO:0005667)cellular_componentA protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
RNA polymerase transcription factor SL1 complex(GO:0005668)cellular_componentA RNA polymerase I-specific transcription factor complex that contains the TATA-box-binding protein (TBP) and at least three TBP-associated factors including proteins known in mammals as TAFI110, TAFI63 and TAFI48.
transcription factor TFIID complex(GO:0005669)cellular_componentA complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.
obsolete transcription-activating factor, 30kD(GO:0005670)cellular_componentOBSOLETE (was not defined before being made obsolete). This term was made obsolete because it represents a single gene product and not a complex.
Ada2/Gcn5/Ada3 transcription activator complex(GO:0005671)cellular_componentA multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues.
transcription factor TFIIA complex(GO:0005672)cellular_componentA component of the transcription machinery of RNA Polymerase II. In humans, TFIIA is a heterotrimer composed of an alpha (P35), beta (P19) and gamma subunits (P12).
transcription factor TFIIE complex(GO:0005673)cellular_componentA transcription factor which in humans consists of a complex of two alpha and two beta chains. Recruits TFIIH to the initiation complex and helps activate both RNA polymerase II and TFIIH.
transcription factor TFIIF complex(GO:0005674)cellular_componentA general transcription initiation factor which in humans consists of a heterodimer of an alpha and a beta subunit. Helps recruit RNA polymerase II to the initiation complex and promotes translation elongation.
transcription factor TFIIH holo complex(GO:0005675)cellular_componentA complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex.
transcription-coupled nucleotide-excision repair(GO:0006283)biological_processThe nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
obsolete positive regulation of transcription of homeotic gene (trithorax group)(GO:0006339)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription of homeotic genes of the trithorax group. This term was made obsolete because it relates to a specific gene family rather than a process.
chromatin-mediated maintenance of transcription(GO:0048096)biological_processMaintenance of transcription by remodelling of chromatin into an 'open configuration'. Once established, this regulation is mitotically stable and is maintained over many cell divisions. It is also heritable.
obsolete negative regulation of transcription of homeotic gene (Polycomb group)(GO:0006340)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription of homeotic genes of the Polycomb group. This term was made obsolete because it relates to a specific gene family rather than a process.
transcription, DNA-templated(GO:0006351)biological_processThe cellular synthesis of RNA on a template of DNA.
DNA-templated transcription, initiation(GO:0006352)biological_processAny process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
DNA-templated transcription, elongation(GO:0006354)biological_processThe extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.
regulation of transcription, DNA-templated(GO:0006355)biological_processAny process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
regulation of transcription by RNA polymerase I(GO:0006356)biological_processAny process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase I.
regulation of transcription by RNA polymerase II(GO:0006357)biological_processAny process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II.
regulation of transcription by RNA polymerase III(GO:0006359)biological_processAny process that modulates the frequency, rate or extent of transcription mediated by RNA ploymerase III.
transcription initiation from RNA polymerase I promoter(GO:0006361)biological_processAny process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
transcription elongation from RNA polymerase I promoter(GO:0006362)biological_processThe extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I.
transcription initiation from RNA polymerase II promoter(GO:0006367)biological_processAny process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
transcription elongation from RNA polymerase II promoter(GO:0006368)biological_processThe extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
transcription initiation from RNA polymerase III promoter(GO:0006384)biological_processAny process involved in the assembly of the RNA polymerase III preinitiation complex (PIC) at an RNA polymerase III promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
transcription elongation from RNA polymerase III promoter(GO:0006385)biological_processThe extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase III promoter by the addition of ribonucleotides catalyzed by RNA polymerase III.
mitochondrial transcription(GO:0006390)biological_processThe synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase.
transcription initiation from mitochondrial promoter(GO:0006391)biological_processA transcription initiation process that takes place at a promoter on the mitochondrial chromosome, and results in RNA synthesis by a mitochondrial RNA polymerase.
transcription elongation from mitochondrial promoter(GO:0006392)biological_processThe extension of an RNA molecule after transcription initiation and promoter clearance at mitochondrial promoter by the addition of ribonucleotides catalyzed by a mitchondrial RNA polymerase.
termination of mitochondrial transcription(GO:0006393)biological_processThe process in which the synthesis of an RNA molecule using a mitochondrial DNA template is completed.
obsolete transcription, RNA-dependent(GO:0006410)biological_processOBSOLETE: The cellular synthesis of DNA on a template of RNA. This term was obsoleted because the name and the definition mean two completely different things: 1) "transcription, RNA-dependent", i.e. RNA-dependent production of an RNA transcript and 2) "reverse transcription", i.e. RNA-dependent DNA synthesis.
DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator(GO:0006978)biological_processA cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the induction of the transcription of p21 (also known as WAF1, CIP1 and SDI1) or any equivalent protein, in response to the detection of DNA damage.
positive regulation of NF-kappaB transcription factor activity by ER overload response(GO:0006985)biological_processThe conversion of inactive NF-kappaB to the active form, thereby allowing it to activate transcription of target genes, as a result of signaling from the endoplasmic reticulum.
obsolete unfolded protein response, cleavage of primary transcript encoding UFP-specific transcription factor(GO:0006988)biological_processOBSOLETE (was not defined before being made obsolete). This term was made obsolete because it represents a function rather than a process.
obsolete unfolded protein response, ligation of mRNA encoding UFP-specific transcription factor by RNA ligase(GO:0006989)biological_processOBSOLETE (was not defined before being made obsolete). This term was made obsolete because it represents a function rather than a process.
positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response(GO:0006990)biological_processThe activation of genes whose promoters contain a specific sequence elements such as the unfolded protein response element (UPRE; consensus CAGCGTG) or the ER stress-response element (ERSE; CCAAN(N)9CCACG), as a result of signaling via the unfolded protein response.
obsolete negative regulation of transcription during mitotic cell cycle(GO:0007068)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
obsolete negative regulation of transcription from RNA polymerase I promoter during mitotic cell cycle(GO:0007069)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase I promoter that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
obsolete negative regulation of transcription from RNA polymerase II promoter during mitotic cell cycle(GO:0007070)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
obsolete negative regulation of transcription from RNA polymerase III promoter during mitotic cell cycle(GO:0007071)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase III promoter that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
positive regulation of transcription involved in exit from mitosis(GO:0007072)biological_processAny process that increases the frequency, rate or extent of transcription as the cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
positive regulation of transcription involved in exit from mitosis, from RNA polymerase I promoter(GO:0007073)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase I promoter as the cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
positive regulation of transcription involved in exit from mitosis, from RNA polymerase II promoter(GO:0007074)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as the cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
positive regulation of transcription involved in exit from mitosis, from RNA polymerase III promoter(GO:0007075)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase III promoter as the cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
positive regulation of transcription of Notch receptor target(GO:0007221)biological_processThe activation of transcription of specific genes as a result of Notch signaling, mediated by the Notch intracellular domain.
positive regulation of hh target transcription factor activity(GO:0007228)biological_processAny process that increases the activity of a transcription factor that activates transcription of Hedgehog-target genes in response to Smoothened signaling. In Drosophila, Cubitus interruptus (Ci) is the only identified transcription factor so far in the Hedgehog signaling pathway. In vertebrates, members of the Gli protein family are activated in this way. Activation of the Gli/Ci transcription factor is distinct from its stabilization, when proteolytic cleavage is inhibited.
positive regulation of transcription from RNA polymerase II promoter by pheromones(GO:0007329)biological_processAny process involving pheromones that activates or increases the rate of transcription from an RNA polymerase II promoter.
positive regulation of central gap gene transcription(GO:0007357)biological_processThe activation of genes encoding transcription factors in the central region of an insect embryo by a combination of maternal regulatory signals and interactions among themselves; exemplified by the activation of expression of the Drosophila Kruppel gene by the hunchback and bicoid gene products.
positive regulation of posterior gap gene transcription(GO:0007360)biological_processThe activation of genes encoding transcription factors in the posterior region of an insect embryo by a combination of maternal regulatory signals and interactions among themselves; exemplified by the activation of expression of the Drosophila knirps gene.
positive regulation of terminal gap gene transcription(GO:0007363)biological_processThe activation of genes encoding transcription factors at the anterior and posterior ends of an insect embryo by a combination of maternal regulatory signals and interactions among themselves; exemplified by the activation of expression of the Drosophila tailless and huckebein genes.
regulation of mating-type specific transcription, DNA-templated(GO:0007532)biological_processAny mating-type specific process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
transcription elongation factor complex(GO:0008023)cellular_componentAny protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation.
cyclin/CDK positive transcription elongation factor complex(GO:0008024)cellular_componentA transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit.
obsolete negative transcription elongation factor activity(GO:0008148)molecular_functionOBSOLETE. Any activity that decreases the rate of transcription elongation, the addition of ribonucleotides to an RNA molecule following transcription initiation. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
negative regulation of DNA-templated transcription, elongation(GO:0032785)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
obsolete positive transcription elongation factor activity(GO:0008159)molecular_functionOBSOLETE. Any activity that increases the rate of transcription elongation, the addition of ribonucleotides to an RNA molecule following transcription initiation. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
positive regulation of DNA-templated transcription, elongation(GO:0032786)biological_processAny process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
mRNA transcription(GO:0009299)biological_processThe cellular synthesis of messenger RNA (mRNA) from a DNA template.
antisense RNA transcription(GO:0009300)biological_processThe synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA.
snRNA transcription(GO:0009301)biological_processThe synthesis of small nuclear RNA (snRNA) from a DNA template.
snoRNA transcription(GO:0009302)biological_processThe synthesis of small nucleolar RNA (snoRNA) from a DNA template.
rRNA transcription(GO:0009303)biological_processThe synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
tRNA transcription(GO:0009304)biological_processThe synthesis of transfer RNA (tRNA) from a DNA template.
positive regulation of transcription by pheromones(GO:0009371)biological_processAny process involving pheromones that activates or increases the rate of transcription.
regulation of transcription by pheromones(GO:0009373)biological_processAny process involving pheromones that modulates the frequency, rate or extent of transcription.
long-distance posttranscriptional gene silencing(GO:0010495)biological_processA posttranscriptional gene silencing process in which the silencing signal originates in a tissue separate from the tissue in which the silencing takes place.
posttranscriptional regulation of gene expression(GO:0010608)biological_processAny process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
mRNA localization resulting in posttranscriptional regulation of gene expression(GO:0010609)biological_processAny process that modulates the frequency, rate or extent of gene expression after the production of a mRNA transcript by its transport into, or maintainance in, a specific location within the cell.
negative regulation of transcription by transcription factor catabolism(GO:0010620)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the catabolism of a sequence-specific DNA-binding transcription factor by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
negative regulation of transcription by transcription factor localization(GO:0010621)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the localization of a transcription factor.
regulation of transcription, start site selection(GO:0010630)biological_processAny process that modulates the frequency, rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA by a mechanism that selects the start site along that template.
regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle(GO:0010672)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as part of the meiotic cell cycle.
positive regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle(GO:0010673)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as part of the meiotic cell cycle.
negative regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle(GO:0010674)biological_processAny process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as part of the meiotic cell cycle.
negative regulation of cellular carbohydrate metabolic process by negative regulation of transcription, DNA-templated(GO:0010678)biological_processAny cellular process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates carried out by repression of transcription.
negative regulation of ribosomal protein gene transcription by RNA polymerase II(GO:0010688)biological_processAny process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes mediated by RNA polymerase II.
negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to chemical stimulus(GO:0010689)biological_processAny process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a chemical stimulus.
negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to stress(GO:0010690)biological_processAny process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a disturbance in organismal or cellular homeostasis.
negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels(GO:0010691)biological_processAny process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
positive regulation of transcription from RNA polymerase II promoter in response to iron(GO:0010723)biological_processAny process that increases the rate of transcription from an RNA polymerase II promoter in response to an iron stimulus.
positive regulation of transcription via serum response element binding(GO:0010735)biological_processAny process that increases the frequency, rate or extent of the specifically regulated synthesis of RNA from DNA encoding a specific set of genes as a result of a transcription factor interacting with a serum response element (SRE). A serum response element is a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum.
regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage(GO:0010767)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus.
negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage(GO:0010768)biological_processAny process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus.
transcription regulatory region DNA binding(GO:0044212)molecular_functionInteracting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
negative regulation of transcription by competitive promoter binding(GO:0010944)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves direct competition for interaction with a promoter binding site.
RNA polymerase II general transcription initiation factor activity(GO:0016251)molecular_functionAn activity that contributes to transcription start site selection and transcription initiation of genes transcribed by RNA polymerase II. The general transcription factors for RNA polymerase II include TFIIB, TFIID, TFIIE, TFIIF, TFIIH and TATA-binding protein (TBP).
obsolete nonspecific RNA polymerase II transcription factor activity(GO:0016252)molecular_functionOBSOLETE. Any function that supports transcription of genes by RNA polymerase II, and is not specific to a particular gene or gene set. This term was obsoleted because "general/nonspecific/basal" transcription vs "specific" transcription were determined not to be separable, distinct process. Thus, terms trying to distinguish "general/nonspecific/basal" transcription from "specific" transcription were removed from both the Molecular Function and the Biological Process ontologies. In addition, this Molecular Function term was defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
posttranscriptional gene silencing(GO:0016441)biological_processThe inactivation of gene expression by a posttranscriptional mechanism.
X chromosome located dosage compensation complex, transcription activating(GO:0016456)cellular_componentAn RNA-protein complex localized to the X chromosome of males where it is required for the hyper-transcriptional activation of the X chromosome. An example of this is found in Drosophila melanogaster.
negative regulation of transcription by RNA polymerase I(GO:0016479)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase I.
negative regulation of transcription by RNA polymerase III(GO:0016480)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase III.
obsolete posttranscriptional insertion or deletion editing(GO:0016551)biological_processOBSOLETE. The insertion into or deletion from an RNA molecule of nucleotide residues not encoded in DNA; takes place after transcription. This term was made obsolete because it represents two separate processes (insertion and deletion).
obsolete cotranscriptional insertion or deletion editing(GO:0016552)biological_processOBSOLETE. The insertion into or deletion from an RNA molecule of nucleotide residues not encoded in DNA; takes place during transcription. This term was made obsolete because it represents two separate processes (insertion and deletion).
obsolete transcription activator activity(GO:0016563)molecular_functionOBSOLETE. Any transcription regulator activity required for initiation or upregulation of transcription. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete transcription repressor activity(GO:0016564)molecular_functionOBSOLETE. Any transcription regulator activity that prevents or downregulates transcription. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete general transcriptional repressor activity(GO:0016565)molecular_functionOBSOLETE. Any activity that stops or downregulates transcription of genes globally, and is not specific to a particular gene or gene set. This term was obsoleted because "general/nonspecific/basal" transcription vs "specific" transcription were determined not to be separable, distinct process. Thus, terms trying to distinguish "general/nonspecific/basal" transcription from "specific" transcription were removed from both the Molecular Function and the Biological Process ontologies. In addition, this Molecular Function term was defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of your repressor is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
negative regulation of transcription, DNA-templated(GO:0045892)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
obsolete specific transcriptional repressor activity(GO:0016566)molecular_functionOBSOLETE. Any activity that stops or downregulates transcription of specific genes or sets of genes. This term was obsoleted because "general/nonspecific/basal" transcription vs "specific" transcription were determined not to be separable, distinct process. Thus, terms trying to distinguish "general/nonspecific/basal" transcription from "specific" transcription were removed from both the Molecular Function and the Biological Process ontologies. In addition, this Molecular Function term was defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of your repressor is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete RNA polymerase I transcription elongation factor activity(GO:0016943)molecular_functionOBSOLETE. Any activity that modulates the rate of transcription elongation, the addition of ribonucleotides to an RNA molecule catalyzed by RNA polymerase I following transcription initiation. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete RNA polymerase II transcription elongation factor activity(GO:0016944)molecular_functionOBSOLETE. Any activity that modulates the rate of transcription elongation, the addition of ribonucleotides to an RNA molecule catalyzed by RNA polymerase II following transcription initiation. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete RNA polymerase III transcription elongation factor activity(GO:0016945)molecular_functionOBSOLETE. Any activity that modulates the rate of transcription elongation, the addition of ribonucleotides to an RNA molecule catalyzed by RNA polymerase III following transcription initiation. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete transcription initiation factor activity(GO:0016986)molecular_functionOBSOLETE. Plays a role in regulating transcription initiation. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
general transcription initiation factor activity(GO:0140223)molecular_functionAn activity that contributes to transcription start site selection and transcription initiation.
obsolete transcription initiation factor antagonist activity(GO:0016988)molecular_functionOBSOLETE. The function of binding to a transcription factor and stopping, preventing or reducing the rate of its transcriptional activity. This term was obsoleted because its definition was vague and apparently broader in scope than the name of the term suggested it was intended to be.
transcriptional repressor complex(GO:0017053)cellular_componentA protein complex that possesses activity that prevents or downregulates transcription.
negative regulation of RNA polymerase II transcriptional preinitiation complex assembly(GO:0017055)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
obsolete basal transcription repressor activity(GO:0017163)molecular_functionOBSOLETE. Any transcription regulator activity that prevents or downregulates basal transcription. Basal transcription results from transcription that is controlled by the minimal complement of proteins necessary to reconstitute transcription from a minimal promoter. This term was obsoleted because "general/nonspecific/basal" transcription vs "specific" transcription were determined not to be separable, distinct process. Thus, terms trying to distinguish "general/nonspecific/basal" transcription from "specific" transcription were removed from both the Molecular Function and the Biological Process ontologies. In addition, this Molecular Function term was defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of your repressor is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
viral transcriptional complex(GO:0019036)cellular_componentSpecific locations and structures in the virus infected cell involved in transcribing the viral genome.
modulation by virus of host transcription(GO:0019056)biological_processAny process in which a virus modulates the frequency, rate or extent of its host's transcription.
viral transcription(GO:0019083)biological_processThe process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
middle viral transcription(GO:0019084)biological_processThe viral transcription that takes place after early transcription in the viral life cycle, and which involves the transcription of genes required for replication.
early viral transcription(GO:0019085)biological_processThe first phase of viral transcription that occurs after entry of the virus into the host cell, but prior to viral genome replication. It involves the transcription of genes for non-structural proteins, and for lytic viruses, the early gene products are involved in establishing control over the host cell.
late viral transcription(GO:0019086)biological_processThe transcription of the final group of viral genes of the viral life cycle, following middle transcription, or where middle transcription doesn't occur, following early transcription. Involves the transcription of genes encoding structural proteins.
regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment(GO:0021882)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a neuroblast to a neuronal fate. The neuron will reside in the forebrain.
regulation of transcription from RNA polymerase II promoter involved in spinal cord anterior-posterior patterning(GO:0021909)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that results in the spatial identity of regions along the anterior-posterior axis of the spinal cord.
regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification(GO:0021912)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that results the commitment of a cell to become a motor neuron in the ventral spinal cord.
regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification(GO:0021913)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that results in the commitment of a cell to become an interneuron in the ventral spinal cord.
regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment(GO:0021918)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of spinal cord motor neurons to specific motor neuron types along the anterior-posterior axis.
regulation of transcription from RNA polymerase II promoter involved in spinal cord association neuron specification(GO:0021920)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of neuronal precursors to association neurons in the dorsal spinal cord.
nuclear receptor transcription coactivator activity(GO:0030374)molecular_functionThe function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
obsolete transcription antiterminator activity(GO:0030401)molecular_functionOBSOLETE. Functions to prevent the termination of RNA synthesis. Acts as a regulatory device, e.g. in phage lambda, enabling a terminator to be masked from RNA polymerase so that distal genes can be expressed. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete transcription regulator activity(GO:0030528)molecular_functionOBSOLETE. Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor. This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
termination of RNA polymerase II transcription, poly(A)-coupled(GO:0030846)biological_processThe process in which transcription of polyadenylated RNA polymerase II transcripts is terminated; cleavage and polyadenylylation of the mRNA 3' end is coupled to transcription termination.
termination of RNA polymerase II transcription, exosome-dependent(GO:0030847)biological_processThe process in which transcription of nonpolyadenylated RNA polymerase II transcripts is terminated; coupled to the maturation of the RNA 3'-end.
MBF transcription complex(GO:0030907)cellular_componentA protein complex that binds to the Mlu1 cell cycle box (MCB) promoter element, consensus sequence ACGCGN, and is involved in regulation of transcription during the G1/S transition of the cell cycle. In Saccharomyces, the complex contains a heterodimer of the DNA binding protein Mbp1p and the activator Swi4p, and is associated with additional proteins known as Nrm1p, Msa1p, and Msa2p; in Schizosaccharomyces the complex contains Res1p, Res2p, and Cdc10p.
regulation of DNA-templated transcription, termination(GO:0031554)biological_processAny process that modulates the frequency, rate, extent, or location of DNA-templated transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
transcriptional attenuation(GO:0031555)biological_processRegulation of transcription through variation in where transcription termination occurs.
transcriptional attenuation by ribosome(GO:0031556)biological_processA type of transcriptional regulation at the level of early termination. This process can occur only in prokaryotes, where transcription of an operon into messenger RNA and translation of that mRNA into polypeptides occur simultaneously. The general principle is that alternative mRNA secondary structures occur under different physiological conditions such as available amount of a particular amino acid. One set of conditions favors early termination of transcription. In the classic example of the trp biosynthesis operon, translation of the gene for a short, trp-containing polypeptide called the trp operon leader peptide pauses either at a trp codon (if tryptophan is scarce) or the stop codon (if trp is readily available). In the former situation transcription continues, but in the latter a Rho-independent terminator forms and reduces, or attenuates, expression of the tryptophan biosynthesis genes. Although the polypeptides encoded by leader peptide genes appear not to be stable once their translation is complete, it is suggested by recent studies that their nascent polypeptide chains interact specifically with ribosomes, specific uncharged tRNAs, or other cellular components to inhibit release at the stop codon and improve the function of transcriptional attenuation as a regulatory switch.
transcription antitermination(GO:0031564)biological_processRegulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
negative regulation of NF-kappaB transcription factor activity(GO:0032088)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
reverse transcription involved in RNA-mediated transposition(GO:0032199)biological_processThe synthesis of DNA from an RNA transposon intermediate.
regulation of DNA-templated transcription, elongation(GO:0032784)biological_processAny process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
negative regulation of CREB transcription factor activity(GO:0032792)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor CREB.
positive regulation of CREB transcription factor activity(GO:0032793)biological_processAny process that activates or increases the frequency, rate or extent of activity of the transcription factor CREB.
negative regulation of viral transcription(GO:0032897)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of viral transcription.
positive regulation of transcription elongation from RNA polymerase II promoter(GO:0032968)biological_processAny process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
regulation of transcription from RNA polymerase II promoter in response to iron ion starvation(GO:0033217)biological_processModulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of iron ions.
transcription factor TFTC complex(GO:0033276)cellular_componentA protein complex that does not contain either a TATA-binding protein (TBP) or a TBP-like factor, but is composed of several TAFIIs and other proteins, including a histone acetyltransferase. This complex is able to nucleate transcription initiation by RNA polymerase II, can mediate transcriptional activation, and has histone acetyltransferase activity.
SBF transcription complex(GO:0033309)cellular_componentA protein complex that binds to the Swi4/6 cell cycle box (SCB) promoter element, consensus sequence CRCGAAA, and activates transcription during the G1/S transition of the cell cycle. In Saccharomyces, the complex contains a heterodimer of the DNA binding protein Swi4p and the activator Swi6p, and is associated with additional proteins known as Whi5p and Msa1p.
co-transcriptional gene silencing by RNA interference machinery(GO:0033562)biological_processA process in which the RNAi machinery mediates the degradation of nascent transcripts in association with chromatin.
activating transcription factor binding(GO:0033613)molecular_functionInteracting selectively and non-covalently with an activating transcription factor, any protein whose activity is required to initiate or upregulate transcription.
regulation of transcription from RNA polymerase II promoter in response to zinc ion starvation(GO:0034225)biological_processModulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is deprived of zinc ions.
regulation of transcription elongation from RNA polymerase II promoter(GO:0034243)biological_processAny process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
negative regulation of transcription elongation from RNA polymerase II promoter(GO:0034244)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
mitochondrial sequence-specific DNA-binding transcription factor activity(GO:0034246)molecular_functionInteracting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by mitochondrial RNA polymerase.
obsolete regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor(GO:0034339)biological_processOBSOLETE. Any process in which a ligand-bound hormone receptor acts in the nucleus to modulate the frequency, rate or extent of transcription from an RNA polymerase II promoter. This term was added by GO_REF:0000021. This term was made obsolete because it is unclear whether the term represents the action of the receptor or the entire process of transcription regulation. The term 'nuclear hormone receptor' is also misleading since many of these receptors reside in the cytoplasm until they are bound by a ligand.
regulation of transcription from RNA polymerase II promoter in response to iron(GO:0034395)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to an iron stimulus.
negative regulation of transcription from RNA polymerase II promoter in response to iron(GO:0034396)biological_processAny process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter in response to an iron stimulus.
chromatin organization involved in regulation of transcription(GO:0034401)biological_processAny cellular process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin that modulates the rate, frequency or extent of DNA-dependent transcription.
transcription factor TFIIIB-alpha complex(GO:0034732)cellular_componentA transcription factor TFIIIB-beta complex that contains the TATA-binding protein (TBP), B'' and a specialized homolog of the conserved subunit BRF referred to as BRFU or TFIIIB50, which found in human but not conserved in yeast; the complex is involved in the regulation of transcription from type 3 (upstream) RNA polymerase III promoters.
transcription factor TFIIIB-beta complex(GO:0034733)cellular_componentA transcription factor TFIIIB-beta complex that contains the TATA-binding protein (TBP), B'' and BRF, and is involved in the regulation of transcription from type 2 RNA polymerase III promoters.
transcription factor TFIIIC1 complex(GO:0034734)cellular_componentA transcription factor complex that forms part of the TFIIIC complex, observed in human. The complex is poorly characterized, but contains the 250-kDa form of HsBdp1, and is thought to include nuclear factor 1 (NF1). It stimulates binding by human TFIIIC2 and is required for transcription activity.
transcription factor TFIIIC2 complex(GO:0034735)cellular_componentA transcription factor complex that forms part of the TFIIIC complex, observed in human; composed of five subunits (GTF3C1/hTFIIIC220/TFIIICalpha, GTF3C2/hTFIIIC110/TFIIICbeta, GTF3C3/hTFIIIC102/TFIIICgamma, GTF3C4/hTFIIIC90/TFIIICdelta and GTF3C5/hTFIIIC63/TFIIICepsilon in human) that together recognize the type 2 RNA polymerase III promoter.
posttranscriptional gene silencing by RNA(GO:0035194)biological_processAny process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation.
transcriptionally active chromatin(GO:0035327)cellular_componentThe ordered and organized complex of DNA and protein that forms regions of the chromosome that are being actively transcribed.
transcriptionally silent chromatin(GO:0035328)cellular_componentThe ordered and organized complex of DNA and protein that forms regions of the chromosome that are not being actively transcribed.
regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter(GO:0035947)biological_processAny process that modulates the frequency, rate or extent of gluconeogenesis, by regulation of transcription from an RNA polymerase II promoter.
positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter(GO:0035948)biological_processAny process that activates or increases the frequency, rate or extent of gluconeogenesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of gluconeogenesis by negative regulation of transcription from RNA polymerase II promoter(GO:0035949)biological_processAny process that activates or increases the frequency, rate or extent of gluconeogenesis by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of oligopeptide transport by regulation of transcription from RNA polymerase II promoter(GO:0035950)biological_processAny process that modulates the frequency, rate or extent of oligopeptide transport, by regulation of transcription from an RNA polymerase II promoter.
positive regulation of oligopeptide transport by positive regulation of transcription from RNA polymerase II promoter(GO:0035951)biological_processAny process that activates or increases the frequency, rate or extent of oligopeptide transport by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of oligopeptide transport by negative regulation of transcription from RNA polymerase II promoter(GO:0035952)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of oligopeptide transport by stopping, preventing or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of dipeptide transport by regulation of transcription from RNA polymerase II promoter(GO:0035953)biological_processAny process that modulates the frequency, rate or extent of dipeptide transport, by regulation of transcription from an RNA polymerase II promoter.
positive regulation of dipeptide transport by positive regulation of transcription from RNA polymerase II promoter(GO:0035954)biological_processAny process that activates or increases the frequency, rate or extent of dipeptide transport by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of dipeptide transport by negative regulation of transcription from RNA polymerase II promoter(GO:0035955)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of dipeptide transport by stopping, preventing or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of starch catabolic process by regulation of transcription from RNA polymerase II promoter(GO:0035956)biological_processAny process that modulates the frequency, rate or extent of the breakdown of starch, by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of starch catabolic process by positive regulation of transcription from RNA polymerase II promoter(GO:0035957)biological_processAny process that activates or increases the frequency, rate or extent of the breakdown of starch, by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of glyoxylate cycle by regulation of transcription from RNA polymerase II promoter(GO:0035958)biological_processAny process that modulates the frequency, rate or extent of the glyoxylate cycle by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of glyoxylate cycle by positive regulation of transcription from RNA polymerase II promoter(GO:0035959)biological_processAny process that activates or increases the frequency, rate or extent of the glyoxylate cycle by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of ergosterol biosynthetic process by regulation of transcription from RNA polymerase II promoter(GO:0035960)biological_processAny process that modulates the frequency, rate or extent of ergosterol biosynthetic process by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of ergosterol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter(GO:0035961)biological_processAny process that activates or increases the frequency, rate or extent of ergosterol biosynthesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of sterol import by regulation of transcription from RNA polymerase II promoter(GO:0035968)biological_processAny process that modulates the frequency, rate or extent of sterol import, by regulation of transcription from an RNA polymerase II promoter.
positive regulation of sterol import by positive regulation of transcription from RNA polymerase II promoter(GO:0035969)biological_processAny process that activates or increases the frequency, rate or extent of sterol import by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
transcription factor AP-1 complex(GO:0035976)cellular_componentA heterodimeric transcription factor complex composed of proteins from the c-Fos, c-Jun, activating transcription factor (ATF) or JDP families. The subunits contain a basic leucine zipper (bZIP) domain that is essential for dimerization and DNA binding. Jun-Fos heterodimers bind preferentially to a heptamer consensus sequence (TPA responsive element (TRE)), whereas Jun-ATF dimers bind the cyclic AMP responsive element (CRE) to regulate transcription of target genes.
positive regulation of transcription from RNA polymerase II promoter in response to stress(GO:0036003)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
positive regulation of unsaturated fatty acid biosynthetic process by positive regulation of transcription from RNA polymerase II promoter(GO:0036083)biological_processAny process that activates or increases the frequency, rate or extent of unsaturated fatty acid biosynthetic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of transcription from RNA polymerase II promoter in response to iron ion starvation(GO:0036086)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of iron ions.
positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress(GO:0036091)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
positive regulation of invasive growth in response to glucose limitation by positive regulation of transcription from RNA polymerase II promoter(GO:0036095)biological_processAny process that activates or increases the frequency, rate or extent of invasive growth as a result of deprivation of glucose, by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of transcription from RNA polymerase II promoter in response to hydrogen peroxide(GO:0036129)biological_processAny process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hydrogen peroxide (H2O2) stimulus.
positive regulation of transcription from RNA polymerase II promoter in response to salt stress(GO:0036251)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under salt stress. The stress is usually an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
positive regulation of transcription from RNA polymerase II promoter in response to menadione(GO:0036252)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a menadione stimulus. Menadione (also called vitamin K3) is a naphthoquinone having a methyl substituent at the 2-position.
positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation(GO:0036278)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a deprivation of nitrogen.
obsolete positive regulation of transcription factor import into nucleus in response to oxidative stress(GO:0036283)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus under conditions of oxidative stress. The reason for obsoletion is that there is no distinct pathway to import transcription factors into the nucleus.
transcription factor catabolic process(GO:0036369)biological_processThe chemical reactions and pathways resulting in the breakdown of a sequence-specific DNA-binding transcription factor by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
RNA polymerase II transcription factor activity, glucocorticoid-activated sequence-specific DNA binding(GO:0038050)molecular_functionCombining with a glucocorticoid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
RNA polymerase II transcription factor activity, estrogen-activated sequence-specific DNA binding(GO:0038052)molecular_functionCombining with estrogen and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
transcription factor activity, estrogen-activated RNA polymerase II transcription factor binding(GO:0038053)molecular_functionCombining with estrogen and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. For example, estrogen-bound receptors can bind to transcription factor complexes to regulate transcription of genes whose promoters do not contain estrogen response elements.
epidermal growth factor receptor signaling pathway via positive regulation of NF-kappaB transcription factor activity(GO:0038167)biological_processThe series of molecular signals generated as a consequence of an epidermal growth factor receptor binding to one of its physiological ligands, where the signal is passed on within the cell via activation of the transcription factor NF-kappaB.
suppression by virus of host transcription initiation from RNA polymerase II promoter(GO:0039602)biological_processAny process in which a virus stops, prevents, or reduces the frequency, rate or extent of the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a host DNA template.
obsolete TBP-class protein binding involved in viral suppression of host transcription initiation from RNA polymerase II promoter(GO:0039603)molecular_functionOBSOLETE. Selective and non-covalent interaction of a viral protein with a member of the class of TATA-binding proteins (TBP) in the host, including any of the TBP-related factors (TRFs), which contributes to the viral-suppression of assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a host DNA template. The reason for obsoletion is that the term is too specific, and the paper referenced in the term should instead be annotated to GO:0039602 suppression by virus of host transcription initiation from RNA polymerase II promoter. See https://github.com/geneontology/go-ontology/issues/14640
obsolete TFIIB-class transcription factor binding involved in viral suppression of host transcription initiation from RNA polymerase II promoter(GO:0039605)molecular_functionOBSOLETE. Selective and non-covalent interaction of a viral protein with a member of the TFIIB-class of host transcription factors, which contributes to the viral-suppression of assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a host DNA template. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
suppression by virus of host NF-kappaB transcription factor activity(GO:0039644)biological_processAny process in which a virus stops, prevents, or reduces the activity of host NF-kappaB activity.
activation by virus of host NF-kappaB transcription factor activity(GO:0039652)biological_processAny process in which a virus starts, promotes, or enhances the activity of the host transcription factor NF-kappaB.
suppression by virus of host transcription(GO:0039653)biological_processAny process in which a virus stops, prevents, or reduces the activity of host DNA-dependent transcription; the cellular synthesis of RNA on a template of DNA. Viral proteins can interfere with either host RNA polymerase or with transcription factors.
viral double stranded DNA replication via reverse transcription(GO:0039688)biological_processA DNA replication process that uses viral RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strands.
DNA-templated viral transcription(GO:0039695)biological_processA transcription process that uses a viral DNA as a template.
RNA-templated viral transcription(GO:0039696)biological_processA transcription process that uses viral RNA as a template.
negative stranded viral RNA transcription(GO:0039697)biological_processA viral transcription process that uses negative stranded (-) single stranded (ss) RNA as a template.
obsolete zinc-mediated transcriptional activator activity(GO:0042156)molecular_functionOBSOLETE. Initiates or upregulates transcription in the presence of zinc. This term was obsoleted because it is defined as a Process term, i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
DNA damage response, signal transduction resulting in transcription(GO:0042772)biological_processA cascade of processes initiated in response to the detection of DNA damage, and resulting in the induction of transcription.
mRNA transcription by RNA polymerase II(GO:0042789)biological_processThe cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.
nucleolar large rRNA transcription by RNA polymerase I(GO:0042790)biological_processThe synthesis of the large ribosomal RNA (rRNA) transcript which encodes several rRNAs, e.g. in mammals 28S, 18S and 5.8S, from a nuclear DNA template transcribed by RNA polymerase I.
5S class rRNA transcription by RNA polymerase III(GO:0042791)biological_processThe synthesis of 5S ribosomal RNA (rRNA), or an equivalent rRNA, from a DNA template by RNA polymerase III (Pol III), originating at a type 1 RNA polymerase III promoter.
mitochondrial rRNA transcription(GO:0042792)biological_processThe synthesis of ribosomal RNA (rRNA) from a mitochondrial DNA template.
plastid transcription(GO:0042793)biological_processThe synthesis of RNA from a plastid DNA template, usually by a specific plastid RNA polymerase.
plastid rRNA transcription(GO:0042794)biological_processThe synthesis of ribosomal RNA (rRNA) from a plastid DNA template, usually by a specific plastid RNA polymerase.
snRNA transcription by RNA polymerase II(GO:0042795)biological_processThe synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
snRNA transcription by RNA polymerase III(GO:0042796)biological_processThe synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase III (Pol III), originating at a Pol III promoter.
tRNA transcription by RNA polymerase III(GO:0042797)biological_processThe synthesis of transfer RNA (tRNA) from a DNA template by RNA polymerase III (Pol III), originating at a Pol III promoter.
obsolete regulation of transcription factor import into nucleus(GO:0042990)biological_processOBSOLETE. Any process that modulates the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. The reason for obsoletion is that there is no distinct pathway to import transcription factors into the nucleus.
obsolete transcription factor import into nucleus(GO:0042991)biological_processOBSOLETE. The directed movement of a transcription factor from the cytoplasm to the nucleus. The reason for obsoletion is that there is no distinct pathway to import transcription factors into the nucleus.
obsolete negative regulation of transcription factor import into nucleus(GO:0042992)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. The reason for obsoletion is that there is no distinct pathway to import transcription factors into the nucleus.
obsolete positive regulation of transcription factor import into nucleus(GO:0042993)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus. The reason for obsoletion is that there is no distinct pathway to import transcription factors into the nucleus.
bHLH transcription factor binding(GO:0043425)molecular_functionInteracting selectively and non-covalently with any of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors, important regulatory components in transcriptional networks of many developmental pathways.
negative regulation of DNA-binding transcription factor activity(GO:0043433)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
regulation of transcription from RNA polymerase II promoter in response to stress(GO:0043618)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
regulation of transcription from RNA polymerase II promoter in response to oxidative stress(GO:0043619)biological_processModulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
regulation of DNA-templated transcription in response to stress(GO:0043620)biological_processModulation of the frequency, rate or extent of transcription from a DNA template as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
modulation by host of viral transcription(GO:0043921)biological_processAny process in which a host organism modulates the frequency, rate or extent of viral transcription.
negative regulation by host of viral transcription(GO:0043922)biological_processAny process in which a host organism stops, prevents, or reduces the frequency, rate or extent of viral transcription.
positive regulation by host of viral transcription(GO:0043923)biological_processAny process in which a host organism activates or increases the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA.
intronic transcription regulatory region DNA binding(GO:0044213)molecular_functionInteracting selectively and non-covalently with an intronic DNA region that regulates the transcription of the transcript it is contained within.
regulation of transcription involved in anterior/posterior axis specification(GO:0044324)biological_processAny process that modulates the frequency, rate or extent of transcription that contributes to the specification of the anterior/posterior axis.
cytoplasmic transcription factor complex(GO:0044797)cellular_componentA protein complex, located in the cytoplasm, that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
nuclear transcription factor complex(GO:0044798)cellular_componentA protein complex, located in the nucleus, that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
carbon catabolite repression of transcription(GO:0045013)biological_processA transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances.
carbon catabolite repression of transcription by glucose(GO:0045014)biological_processA transcription regulation process in which the presence of glucose leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances.
obsolete regulation of transcription of homeotic gene (Polycomb group)(GO:0045888)biological_processOBSOLETE. Any process that modulates the frequency, rate or extent of transcription of homeotic genes of the Polycomb group. This term was made obsolete because it relates to a specific gene family rather than a process.
obsolete positive regulation of transcription of homeotic gene (Polycomb group)(GO:0045889)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription of homeotic genes of the Polycomb group. This term was made obsolete because it relates to a specific gene family rather than a process.
obsolete regulation of transcription of homeotic gene (trithorax group)(GO:0045890)biological_processOBSOLETE. Any process that modulates the frequency, rate or extent of transcription of homeotic genes of the trithorax group. This term was made obsolete because it relates to a specific gene family rather than a process.
obsolete negative regulation of transcription of homeotic gene (trithorax group)(GO:0045891)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription of homeotic genes of the trithorax group. This term was made obsolete because it relates to a specific gene family rather than a process.
positive regulation of transcription, DNA-templated(GO:0045893)biological_processAny process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
negative regulation of mating-type specific transcription, DNA-templated(GO:0045894)biological_processAny mating-type specific process that stops, prevents or reduces the rate of cellular DNA-templated transcription.
positive regulation of mating-type specific transcription, DNA-templated(GO:0045895)biological_processAny mating-type specific process that activates or increases the rate of cellular DNA-templated transcription.
obsolete regulation of transcription during mitotic cell cycle(GO:0045896)biological_processOBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
obsolete positive regulation of transcription during mitotic cell cycle(GO:0045897)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
regulation of RNA polymerase II transcriptional preinitiation complex assembly(GO:0045898)biological_processAny process that modulates the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
positive regulation of RNA polymerase II transcriptional preinitiation complex assembly(GO:0045899)biological_processAny process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
positive regulation of transcription by RNA polymerase I(GO:0045943)biological_processAny process that activates or increases the frequency, rate or extent of transcription mediated by RNA polymerase I.
positive regulation of transcription by RNA polymerase II(GO:0045944)biological_processAny process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of transcription by RNA polymerase III(GO:0045945)biological_processAny process that activates or increases the frequency, rate or extent of transcription mediated by RNA polymerase III.
carbon catabolite regulation of transcription(GO:0045990)biological_processA transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources.
carbon catabolite activation of transcription(GO:0045991)biological_processA transcription regulation process in which the presence of one carbon source leads to an increase in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources.
negative regulation of transcription by pheromones(GO:0045996)biological_processAny process involving pheromones that stops, prevents or reduces the rate of transcription.
regulation of transcription by glucose(GO:0046015)biological_processAny process involving glucose that modulates the frequency, rate or extent or transcription.
positive regulation of transcription by glucose(GO:0046016)biological_processAny process involving glucose that activates or increases the rate of transcription.
obsolete regulation of transcription from RNA polymerase I promoter during mitotic cell cycle(GO:0046017)biological_processOBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
obsolete positive regulation of transcription from RNA polymerase I promoter during mitotic cell cycle(GO:0046018)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase I promoter that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
regulation of transcription from RNA polymerase II promoter by pheromones(GO:0046019)biological_processAny process involving pheromones that modulates the frequency, rate or extent or transcription from an RNA polymerase II promoter.
negative regulation of transcription from RNA polymerase II promoter by pheromones(GO:0046020)biological_processAny process involving pheromones that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
obsolete regulation of transcription from RNA polymerase II promoter during mitotic cell cycle(GO:0046021)biological_processOBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
obsolete positive regulation of transcription from RNA polymerase II promoter during mitotic cell cycle(GO:0046022)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
obsolete regulation of transcription from RNA polymerase III promoter during mitotic cell cycle(GO:0046023)biological_processOBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase III promoter that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
obsolete positive regulation of transcription from RNA polymerase III promoter during mitotic cell cycle(GO:0046024)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III that occurs during the mitotic cell cycle. The reason for obsoletion is that 'during' should be captured using an annotation extension. See also comments here: https://github.com/geneontology/go-ontology/issues/14896
regulation of viral transcription(GO:0046782)biological_processAny process that modulates the frequency, rate or extent of the transcription of the viral genome.
positive regulation of viral transcription(GO:0050434)biological_processAny process that activates or increases the frequency, rate or extent of viral transcription.
regulation of transcription involved in meiotic cell cycle(GO:0051037)biological_processAny process that modulates the frequency, rate or extent of transcription as part of a meiotic cell cycle.
negative regulation of transcription involved in meiotic cell cycle(GO:0051038)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of transcription involved in the meiotic cell cycle.
positive regulation of transcription involved in meiotic cell cycle(GO:0051039)biological_processAny process that activates or increases the frequency, rate or extent of transcription as part of a meiotic cell cycle.
regulation of DNA-binding transcription factor activity(GO:0051090)biological_processAny process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
positive regulation of DNA-binding transcription factor activity(GO:0051091)biological_processAny process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
positive regulation of NF-kappaB transcription factor activity(GO:0051092)biological_processAny process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
modulation by symbiont of host transcription(GO:0052026)biological_processAny process in which an organism modulates the frequency, rate or extent of its host's transcription. The host is defined as the larger of the organisms involved in a symbiotic interaction.
modulation of transcription in other organism involved in symbiotic interaction(GO:0052312)biological_processAny process in which an organism modulates the frequency, rate or extent of transcription in a second organism, where the two organisms are in a symbiotic interaction.
modulation by host of symbiont transcription(GO:0052472)biological_processAny process in which an organism modulates the frequency, rate or extent of its symbiont's transcription.
regulation of posttranscriptional gene silencing(GO:0060147)biological_processAny process that modulates the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism.
positive regulation of posttranscriptional gene silencing(GO:0060148)biological_processAny process that increases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism.
negative regulation of posttranscriptional gene silencing(GO:0060149)biological_processAny process that decreases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism.
regulation of antisense RNA transcription(GO:0060194)biological_processAny process that modulates the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA.
negative regulation of antisense RNA transcription(GO:0060195)biological_processAny process that decreases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA.
positive regulation of antisense RNA transcription(GO:0060196)biological_processAny process that increases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA.
regulation of transcription initiation from RNA polymerase II promoter(GO:0060260)biological_processAny process that modulates the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
positive regulation of transcription initiation from RNA polymerase II promoter(GO:0060261)biological_processAny process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
obsolete negative regulation of transcription involved in G1 phase of mitotic cell cycle(GO:0060277)biological_processOBSOLETE. Any process that stop, prevents or decreases transcription as part of the G1 phase of the mitotic cell cycle. This term was made obsolete because it is unclear exactly what it means. It could mean either 'regulation of transcription during phase X' or 'regulation of transition between phase X and phase Y'.
negative regulation of transcription involved in G1/S transition of mitotic cell cycle(GO:0071930)biological_processAny process that stop, prevents or decreases transcription as part of the G1/S transition of the mitotic cell cycle.
positive regulation of transcription involved in egg activation(GO:0060469)biological_processAny process that increases the rate, frequency or extent of transcription as a part of the process of egg activation.
regulation of transcription from RNA polymerase II promoter involved in lung bud formation(GO:0060500)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the branching morphogenesis by which the initial primordium of the lung is formed.
positive regulation of DNA-templated transcription, termination(GO:0060566)biological_processAny process that increases the rate, frequency or extent of DNA-templated transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
negative regulation of DNA-templated transcription, termination(GO:0060567)biological_processAny process that decreases the rate, frequency or extent of DNA-dependent transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
regulation of transcription from RNA polymerase II promoter involved in mammary gland formation(GO:0060597)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the formation of the mammary line, placode or bud.
negative regulation of transcription initiation from RNA polymerase II promoter(GO:0060633)biological_processAny process that decreases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
regulation of transcription involved in primary germ layer cell fate commitment(GO:0060796)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that results in cells adopting an endoderm, ectoderm or mesoderm cell fate.
negative regulation of trophoblast cell differentiation by transcription regulation from RNA polymerase II promoter(GO:0060805)biological_processAny process that modulates the rate, frequency or extent of transcription from an RNA polymerase II promoter ultimately resulting in a decrease in trophoblast stem cells differentiating into the more mature cells of the trophoblast.
regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification(GO:0060807)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that ultimately results in a cell being specified to adopt a definitive endodermal cell fate.
regulation of transcription involved in lymphatic endothelial cell fate commitment(GO:0060849)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a venous endothelial cell to a lymphatic endothelial cell.
regulation of transcription involved in cell fate commitment(GO:0060850)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a cell to a specific fate.
regulation of transcription involved in venous endothelial cell fate commitment(GO:0060852)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a cell to a specific fate and contributes to a cell adopting a venous endothelial cell fate.
regulation of transcription involved in eye field cell fate commitment of camera-type eye(GO:0060899)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a neurectodermal cell to a specialized neurectodermal cell that will give rise to the optic vesicle.
regulation of ribosomal protein gene transcription by RNA polymerase II(GO:0060962)biological_processAny process that modulates the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes mediated by RNA polymerase II.
positive regulation of ribosomal protein gene transcription by RNA polymerase II(GO:0060963)biological_processAny process that increases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes mediated by RNA polymerase II.
regulation of transcription from RNA polymerase II promoter involved in kidney development(GO:0060994)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the branching morphogenesis by which the kidney progresses from its initial formation to the mature state.
regulation of transcription from RNA polymerase II promoter involved in mesonephros development(GO:0061216)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the mesonephros progressing from its initial formation to the mature state.
regulation of transcription from RNA polymerase II promoter in response to osmotic stress(GO:0061392)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
positive regulation of transcription from RNA polymerase II promoter in response to osmotic stress(GO:0061393)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance(GO:0061394)biological_processModulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
positive regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance(GO:0061395)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
regulation of transcription from RNA polymerase II promoter in response to copper ion(GO:0061396)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to an copper ion stimulus.
positive regulation of transcription from RNA polymerase II promoter in response to copper ion(GO:0061397)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to an copper ion stimulus.
negative regulation of transcription from RNA polymerase II promoter in response to copper ion(GO:0061398)biological_processAny process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to an copper ion stimulus.
positive regulation of transcription from RNA polymerase II promoter in response to cobalt ion(GO:0061399)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a cobalt ion stimulus.
positive regulation of transcription from RNA polymerase II promoter in response to calcium ion(GO:0061400)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a calcium ion stimulus.
positive regulation of transcription from RNA polymerase II promoter in response to a hypotonic environment(GO:0061401)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of detection of, or exposure to, a decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
positive regulation of transcription from RNA polymerase II promoter in response to acidic pH(GO:0061402)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a pH stimulus with pH < 7.
positive regulation of transcription from RNA polymerase II promoter in response to nitrosative stress(GO:0061403)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
positive regulation of transcription from RNA polymerase II promoter in response to increased salt(GO:0061404)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of detection of, or exposure to, an increase in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
positive regulation of transcription from RNA polymerase II promoter in response to hydrostatic pressure(GO:0061405)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hydrostatic pressure stimulus. Hydrostatic pressure is the force acting on an object in a system where the fluid is at rest (as opposed to moving). The weight of the fluid above the object creates pressure on it.
positive regulation of transcription from RNA polymerase II promoter in response to glucose starvation(GO:0061406)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of glucose.
positive regulation of transcription from RNA polymerase II promoter in response to hydrogen peroxide(GO:0061407)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hydrogen peroxide (H2O2) stimulus.
positive regulation of transcription from RNA polymerase II promoter in response to heat stress(GO:0061408)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
positive regulation of transcription from RNA polymerase II promoter in response to freezing(GO:0061409)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a freezing stimulus, temperatures below 0 degrees Celsius.
positive regulation of transcription from RNA polymerase II promoter in response to ethanol(GO:0061410)biological_processAny process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an ethanol stimulus.
positive regulation of transcription from RNA polymerase II promoter in response to cold(GO:0061411)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation(GO:0061412)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of amino acids.
regulation of transcription from RNA polymerase II promoter by a nonfermentable carbon source(GO:0061413)biological_processA transcription regulation process in which the presence of a nonfermentable carbon source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources.
positive regulation of transcription from RNA polymerase II promoter by a nonfermentable carbon source(GO:0061414)biological_processA transcription regulation process in which the presence of a nonfermentable carbon source leads to an increase of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources.
negative regulation of transcription from RNA polymerase II promoter by a nonfermentable carbon source(GO:0061415)biological_processA transcription regulation process in which the presence of a nonfermentable carbon source leads to a decrease of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources.
regulation of transcription from RNA polymerase II promoter in response to salt stress(GO:0061416)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under salt stress. The stress is usually an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
negative regulation of transcription from RNA polymerase II promoter in response to oxidative stress(GO:0061417)biological_processAny process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
regulation of transcription from RNA polymerase II promoter in response to hypoxia(GO:0061418)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
positive regulation of transcription from RNA polymerase II promoter in response to hypoxia(GO:0061419)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
regulation of transcription from RNA polymerase II promoter in response to biotin starvation(GO:0061420)biological_processModulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of biotin.
positive regulation of transcription by oleic acid(GO:0061421)biological_processAny process involving oleic acid that activates or increases the rate of transcription.
positive regulation of transcription from RNA polymerase II promoter in response to alkaline pH(GO:0061422)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a pH >7.0.
positive regulation of sodium ion transport by positive regulation of transcription from RNA polymerase II promoter(GO:0061423)biological_processAny process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter resulting in the increased frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of peroxisome organization by positive regulation of transcription from RNA polymerase II promoter(GO:0061424)biological_processAny process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter and activates or increases the frequency, rate or extent of peroxisome organization.
positive regulation of ethanol catabolic process by positive regulation of transcription from RNA polymerase II promoter(GO:0061425)biological_processAny process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter and activates or increases the frequency, rate or extent of an ethanol catabolic process.
positive regulation of sulfite transport by positive regulation of transcription from RNA polymerase II promoter(GO:0061426)biological_processAny process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter and activates or increases the frequency, rate or extent of sulfite transport.
negative regulation of ceramide biosynthetic process by negative regulation of transcription from RNA Polymerase II promoter(GO:0061427)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter and stops, prevents or reduces the frequency, rate or extent of a ceramide biosynthetic process.
negative regulation of transcription from RNA polymerase II promoter in response to hypoxia(GO:0061428)biological_processAny process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
positive regulation of transcription from RNA polymerase II promoter by oleic acid(GO:0061429)biological_processAny process involving oleic acid that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of transcription from RNA polymerase II promoter in response to methionine(GO:0061432)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a methionine stimulus.
regulation of replicative cell aging by regulation of transcription from RNA polymerase II promoter in response to caloric restriction(GO:0061434)biological_processAny process that modulates the frequency, rate or extent of replicative cell aging through a mechanism that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a caloric restriction stimulus.
positive regulation of transcription from a mobile element promoter(GO:0061435)biological_processAny process that activates or increases the frequency, rate or extent of transcription from a mobile element promoter.
positive regulation of transcription by transcription factor localization(GO:0061586)biological_processAny process that activates or increases the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the localization of a transcription factor.
pri-miRNA transcription by RNA polymerase II(GO:0061614)biological_processThe cellular synthesis of primary microRNA (pri-miRNA) transcripts from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. pri-miRNA transcripts are subsequently processed to produce the ~22nt miRNAs that function in gene regulation.
RNA polymerase II sequence-specific DNA-binding transcription factor binding(GO:0061629)molecular_functionInteracting selectively and non-covalently with a sequence-specific DNA binding RNA polymerase II transcription factor, any of the factors that interact selectively and non-covalently with a specific DNA sequence in order to modulate transcription.
negative regulation of transcription by glucose(GO:0061986)biological_processAny process involving glucose that decreases the frequency, rate or extent or transcription.
negative regulation of transcription from RNA polymerase II promoter by glucose(GO:0061987)biological_processAny process involving glucose that decreases the frequency, rate or extent or transcription from an RNA polymerase II promoter.
transcription factor TFIIH holo complex binding(GO:0062058)molecular_functionInteracting selectively and non-covalently with a transcription factor TFIIH holo complex.
regulation of transcription by carbon monoxide(GO:0070028)biological_processAny process involving carbon monoxide that modulates the frequency, rate or extent of transcription.
transcription factor TFIIIB complex assembly(GO:0070217)biological_processThe aggregation, arrangement and bonding together of a set of components to form a transcription factor TFIIIB complex.
transcription factor TFIIIE complex(GO:0070264)cellular_componentA transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIE contains a specific subset of ribosomal proteins.
transcription export complex 2(GO:0070390)cellular_componentA protein complex that couples SAGA-dependent gene expression to mRNA export at the inner side of the nuclear pore complex (NPC). The TREX-2 complex is tethered to the inner side of the NPC via the nucleoporins Nup1 and Nup60; in S. cerevisiae it contains Sac3p, Thp1p, Sem1, Sus1p and Cdc31p.
repressing transcription factor binding(GO:0070491)molecular_functionInteracting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
TAF4B-containing transcription factor TFIID complex(GO:0070556)cellular_componentA transcription factor TFIID complex that contains the TBP-associated factor TAF4B (also known as TAFII105 in human), a cell-type-specific variant of TAF4.
transcription preinitiation complex assembly(GO:0070897)biological_processThe aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), required for transcription.
transcription factor TFIIK complex(GO:0070985)cellular_componentA transcription factor complex that forms part of the holo TFIIH complex. In Saccharomyces/human, TFIIK contains Ccl1p/Cyclin H, Tfb3p/MAT1 and Kin2p/CDK7.
nuclear retention of pre-mRNA at the site of transcription(GO:0071033)biological_processThe process involved in retention of aberrant or improperly formed mRNAs, e.g. those that are incorrectly or incompletely spliced or that have incorrectly formed 3'-ends, within the nucleus at the site of transcription.
nuclear retention of unspliced pre-mRNA at the site of transcription(GO:0071048)biological_processThe process involved in retention of incorrectly or incompletely spliced pre-mRNA within the nucleus at the site of transcription.
nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription(GO:0071049)biological_processThe process involved in retention of mRNAs that have incorrectly formed 3'-ends within the nucleus at the site of transcription.
transcriptional activation by promoter-enhancer looping(GO:0071733)biological_processThe formation and maintenance of DNA loops that juxtapose the promoter and enhancer regions of RNA polymerase II-transcribed genes and activate transcription from an RNA polymerase II promoter.
positive regulation of transcription involved in G1/S transition of mitotic cell cycle(GO:0071931)biological_processAny process that activates or increases transcription as part of the G1/S transition of the mitotic cell cycle.
regulation of transcription from RNA polymerase II promoter involved in metanephros development(GO:0072212)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the branching morphogenesis by which the metanephros progresses from its initial formation to the mature state.
regulation of glycolytic process by regulation of transcription from RNA polymerase II promoter(GO:0072361)biological_processAny process that modulates the frequency, rate or extent of glycolysis by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter(GO:0072362)biological_processAny process that modulates the frequency, rate or extent of glycolysis by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of glycolytic process by positive regulation of transcription from RNA polymerase II promoter(GO:0072363)biological_processAny process that modulates the frequency, rate or extent of glycolysis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of cellular ketone metabolic process by regulation of transcription from RNA polymerase II promoter(GO:0072364)biological_processAny process that modulates the frequency, rate or extent of a cellular ketone metabolic process by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter(GO:0072365)biological_processAny process that modulates the frequency, rate or extent of a cellular ketone metabolic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter(GO:0072366)biological_processAny process that modulates the frequency, rate or extent of a cellular ketone metabolic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of lipid transport by regulation of transcription from RNA polymerase II promoter(GO:0072367)biological_processAny process that modulates the frequency, rate or extent of lipid transport by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter(GO:0072368)biological_processAny process that modulates the frequency, rate or extent of lipid transport by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter(GO:0072369)biological_processAny process that modulates the frequency, rate or extent of lipid transport by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
obsolete negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor(GO:0072500)biological_processOBSOLETE. Any process in which a ligand-bound hormone receptor acts in the nucleus to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. This term was made obsolete because it is unclear whether the term represents the action of the receptor or the entire process of transcription regulation. The term 'nuclear hormone receptor' is also misleading since many of these receptors reside in the cytoplasm until they are bound by a ligand.
SAGA complex localization to transcription regulatory region(GO:0072742)biological_processAny process in which a SAGA complex is transported to, or maintained in, a specific location in the transcription regulatory region of a gene.
regulation of transcription in response to host(GO:0075180)biological_processAny process in which the symbiont organism modulates the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
positive regulation of symbiont transcription in response to host(GO:0075181)biological_processAny process in which an organism activates, maintains or increases the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
negative regulation of symbiont transcription in response to host(GO:0075182)biological_processAny process in which an organism stops, prevents, or reduces the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
regulation of transcription involved in anterior neural plate formation(GO:0090019)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter contributing to the formation of the anterior neural plate.
regulation of transcription involved in posterior neural plate formation(GO:0090020)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter contributing to the formation of the posterior neural plate.
obsolete regulation of transcription regulator activity(GO:0090046)biological_processOBSOLETE. Any process that modulates the frequency, rate or extent of transcription regulator activity, any molecular function that plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor. At the time of obsoletion, under "regulation of molecular function", a term exists for "regulation of sequence-specific DNA-binding transcription factor activity" and the positive and negative child terms, but no more detailed terms exist. In reannotating, please consider if the paper would support annotation to a regulation term for a specific RNA polymerase. Also consider if what you need would be regulation of protein binding transcription factor activity or any of its child terms instead. If so, please consider making a SF item regarding creation of such a term.
obsolete positive regulation of transcription regulator activity(GO:0090047)biological_processOBSOLETE. Any process that increases the frequency, rate or extent of transcription regulator activity, any molecular function that plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor. At the time of obsoletion, under "regulation of molecular function", a term exists for "regulation of sequence-specific DNA-binding transcription factor activity" and the positive and negative child terms, but no more detailed terms exist. In reannotating, please consider if the paper would support annotation to a regulation term for a specific RNA polymerase. Also consider if what you need would be regulation of protein binding transcription factor activity or any of its child terms instead. If so, please consider making a SF item regarding creation of such a term.
obsolete negative regulation of transcription regulator activity(GO:0090048)biological_processOBSOLETE. Any process that decreases the frequency, rate or extent of transcription regulator activity, any molecular function that plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor. At the time of obsoletion, under "regulation of molecular function", a term exists for "regulation of sequence-specific DNA-binding transcription factor activity" and the positive and negative child terms, but no more detailed terms exist. In reannotating, please consider if the paper would support annotation to a regulation term for a specific RNA polymerase. Also consider if what you need would be regulation of protein binding transcription factor activity or any of its child terms instead. If so, please consider making a SF item regarding creation of such a term.
transcriptional activation by promoter-terminator looping(GO:0090203)biological_processThe formation and maintenance of DNA loops that juxtapose the promoter and terminator regions of RNA polymerase II-transcribed genes and activate transcription from an RNA polymerase II promoter.
regulation of transcription from RNA polymerase II promoter involved in somitogenesis(GO:0090236)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
regulation of transcription-coupled nucleotide-excision repair(GO:0090262)biological_processAny process that modulates the frequency, rate, or extent of the nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
positive regulation of transcription involved in G2/M transition of mitotic cell cycle(GO:0090282)biological_processAny process that activates or increases the frequency, rate or extent of transcription of target genes that are transcribed as part of the G2/M transition of the mitotic cell cycle.
nitrogen catabolite regulation of transcription(GO:0090293)biological_processA transcription regulation process in which the presence of one nitrogen source leads to the modulation of the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources.
nitrogen catabolite activation of transcription(GO:0090294)biological_processA transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources.
nitrogen catabolite repression of transcription(GO:0090295)biological_processA transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources.
negative regulation of transcription from RNA polymerase II promoter in response to iron ion starvation(GO:0090375)biological_processAny process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of iron ions.
obsolete positive regulation of transcription from RNA polymerase II promoter involved in fatty acid biosynthetic process(GO:0090412)biological_processAny positive regulation of transcription from RNA polymerase II promoter that is involved in fatty acid biosynthetic process.
obsolete negative regulation of transcription from RNA polymerase II promoter involved in fatty acid biosynthetic process(GO:0090413)biological_processAny negative regulation of transcription from RNA polymerase II promoter that is involved in fatty acid biosynthetic process.
obsolete positive regulation of transcription involved in S-phase of mitotic cell cycle(GO:0090418)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription of target genes that are transcribed as part of the S phase of the mitotic cell cycle. This term was made obsolete because it is unclear exactly what it means. It could mean either 'regulation of transcription during phase X' or 'regulation of transition between phase X and phase Y'.
negative regulation of transcription involved in G2/M transition of mitotic cell cycle(GO:0090419)biological_processAny process that inhibits or decreases the frequency, rate or extent of transcription of target genes that are transcribed as part of the G2/M transition of the mitotic cell cycle.
nuclear transcriptional repressor complex(GO:0090568)cellular_componentA protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription.
cytoplasmic transcriptional repressor complex(GO:0090569)cellular_componentA protein complex, located in the cytoplasm, that possesses activity that prevents or downregulates transcription.
RNA polymerase I transcription repressor complex(GO:0090570)cellular_componentA protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription from a RNA polymerase I promoter.
RNA polymerase II transcription repressor complex(GO:0090571)cellular_componentA protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription from a RNA polymerase II promoter.
RNA polymerase III transcription repressor complex(GO:0090572)cellular_componentA protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription from a RNA polymerase III promoter.
RNA polymerase IV transcription repressor complex(GO:0090573)cellular_componentA protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription from a RNA polymerase IV promoter.
RNA polymerase V transcription repressor complex(GO:0090574)cellular_componentA protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription from a RNA polymerase V promoter.
RNA polymerase II transcription factor complex(GO:0090575)cellular_componentA transcription factor complex that acts at a regulatory region of a gene transcribed by RNA polymerase II.
RNA polymerase III transcription factor complex(GO:0090576)cellular_componentA transcription factor complex that acts at a regulatory region of a gene transcribed by RNA polymerase III.
RNA polymerase IV transcription factor complex(GO:0090577)cellular_componentA transcription factor complex that acts at a regulatory region of a gene transcribed by RNA polymerase IV.
RNA polymerase V transcription factor complex(GO:0090578)cellular_componentA transcription factor complex that acts at a regulatory region of a gene transcribed by RNA polymerase V.
negative regulation of transcription from RNA polymerase II promoter in response to stress(GO:0097201)biological_processAny process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
M/G1 phase-specific MADS box-forkhead transcription factor complex(GO:0097221)cellular_componentA protein complex that contains a MADS-box protein and two forkhead domain proteins, and binds to and regulates transcription from promoters of genes transcribed during the M/G1 transition of the cell cycle. In Schizosaccharomyces pombe, the complex contains the MADS-box protein Mbx1 and two forkhead proteins, Sep1 and Fkh2.
positive regulation of fatty acid beta-oxidation by positive regulation of transcription from RNA polymerase II promoter(GO:0097235)biological_processAny process that activates or increases the frequency, rate or extent of fatty acid beta-oxidation by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of transcription from RNA polymerase II promoter in response to zinc ion starvation(GO:0097236)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of zinc ions.
positive regulation of transcription from RNA polymerase II promoter in response to methylglyoxal(GO:0097239)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a methylglyoxal stimulus.
regulation of potassium ion concentration by positive regulation of transcription from RNA polymerase II promoter(GO:0097301)biological_processAny process that regulates the internal concentration of potassium ions at the level of a cell by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
telomeric repeat-containing RNA transcription(GO:0097393)biological_processThe synthesis of telomeric repeat-containing RNA from a DNA template. A telomere is a complex of DNA and proteins that seals the end of a chromosome.
telomeric repeat-containing RNA transcription by RNA polymerase II(GO:0097394)biological_processThe synthesis of telomeric repeat-containing RNA from a DNA template by RNA polymerase II (Pol II), originating at a Pol II promoter.
transcription ternary complex(GO:0097523)cellular_componentA protein-DNA-RNA complex composed of RNA polymerase, template DNA, and an RNA transcript.
chromatin organization involved in negative regulation of transcription(GO:0097549)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of transcription by chromatin organization.
transcriptional preinitiation complex(GO:0097550)cellular_componentA protein-DNA complex composed of proteins binding promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription.
nucleic acid-templated transcription(GO:0097659)biological_processThe cellular synthesis of RNA on a template of nucleic acid (DNA or RNA).
transcription factor activity, direct ligand regulated sequence-specific DNA binding(GO:0098531)molecular_functionA DNA-binding transcription factor activity that is directly regulated by binding of a ligand to the protein with this activity. Examples include the lac and trp repressors in E.coli and many steroid hormone receptors.
regulation of carbohydrate catabolic process by regulation of transcription from RNA polymerase II promoter(GO:0098679)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of carbohydrate catabloism.
ncRNA transcription(GO:0098781)biological_processThe transcription of non (protein) coding RNA from a DNA template.
ncRNA transcription associated with protein coding gene TSS/TES(GO:0098790)biological_processThe transcription of non-coding RNA associated with transcriptional start and end sites of protein coding genes. This occurs at some low level for many protein coding genes.
obsolete transcriptional repressor activity, RNA polymerase II activating transcription factor binding(GO:0098811)molecular_functionOBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II activating transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent. For more details see https://github.com/geneontology/go-ontology/issues/16053
positive regulation of sodium ion transport by transcription from RNA polymerase II promoter(GO:0100003)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates sodium ion transport
positive regulation of peroxisome organization by transcription from RNA polymerase II promoter(GO:0100004)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates peroxisome organization
positive regulation of ethanol catabolic process by transcription from RNA polymerase II promoter(GO:0100005)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates ethanol catabolic process
positive regulation of sulfite transport by transcription from RNA polymerase II promoter(GO:0100006)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates sulfite transport
negative regulation of ceramide biosynthetic process by transcription from RNA polymerase II promoter(GO:0100007)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates ceramide biosynthetic process
positive regulation of fatty acid beta-oxidation by transcription from RNA polymerase II promoter(GO:0100013)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates fatty acid beta-oxidation
positive regulation of mating type switching by transcription from RNA polymerase II promoter(GO:0100014)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates mating type switching
positive regulation of inositol biosynthetic process by transcription from RNA polymerase II promoter(GO:0100015)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates inositol biosynthetic process
regulation of thiamine biosynthetic process by transcription from RNA polymerase II promoter(GO:0100016)biological_processAny transcription from RNA polymerase II promoter process that regulates thiamine biosynthetic process
negative regulation of cell-cell adhesion by transcription from RNA polymerase II promoter(GO:0100017)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates single organismal cell-cell adhesion
regulation of glucose import by transcription from RNA polymerase II promoter(GO:0100018)biological_processAny transcription from RNA polymerase II promoter process that regulates glucose import
obsolete regulation of cAMP-mediated signaling by transcription from RNA polymerase II promoter(GO:0100019)biological_processOBSOLETE. Any transcription from RNA polymerase II promoter process that regulates cAMP-mediated signaling The reason for obsoletion is that cAMP-mediated signaling is not mediated by transcription from RNA polII promoter. Consistent with this, there were no annotations to the term. https://github.com/geneontology/go-ontology/issues/14279
regulation of transport by transcription from RNA polymerase II promoter(GO:0100020)biological_processAny transcription from RNA polymerase II promoter process that regulates transport
regulation of iron ion transport by transcription from RNA polymerase II promoter(GO:0100021)biological_processAny transcription from RNA polymerase II promoter process that regulates iron ion transport
regulation of iron ion import by transcription from RNA polymerase II promoter(GO:0100022)biological_processAny transcription from RNA polymerase II promoter process that regulates iron ion import
regulation of meiotic nuclear division by transcription from RNA polymerase II promoter(GO:0100023)biological_processAny transcription from RNA polymerase II promoter process that regulates meiotic nuclear division
regulation of carbohydrate metabolic process by transcription from RNA polymerase II promoter(GO:0100024)biological_processAny transcription from RNA polymerase II promoter process that regulates carbohydrate metabolic process
negative regulation of cellular amino acid biosynthetic process by transcription from RNA polymerase II promoter(GO:0100025)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates cellular amino acid biosynthetic process
positive regulation of DNA repair by transcription from RNA polymerase II promoter(GO:0100026)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates DNA repair
obsolete regulation of cell separation after cytokinesis by transcription from RNA polymerase II promoter(GO:0100027)biological_processOBSOLETE Any transcription from RNA polymerase II promoter process that regulates cell separation after cytokinesis
regulation of conjugation with cellular fusion by transcription from RNA polymerase II promoter(GO:0100028)biological_processAny transcription from RNA polymerase II promoter process that regulates conjugation with cellular fusion
obsolete regulation of histone modification by transcription from RNA polymerase II promoter(GO:0100029)biological_processOBSOLETE. Any transcription from RNA polymerase II promoter process that regulates histone modification. This term was obsoleted because it describes a process that does not exist.
obsolete regulation of histone acetylation by transcription from RNA polymerase II promoter(GO:0100030)biological_processOBSOLETE. Any transcription from RNA polymerase II promoter process that regulates histone acetylation. This term was obsoleted because it describes a process that does not exist.
obsolete regulation of histone methylation by transcription from RNA polymerase II promoter(GO:0100031)biological_processOBSOLETE. Any transcription from RNA polymerase II promoter process that regulates histone methylation. This term was obsoleted because it describes a process that does not exist.
positive regulation of phospholipid biosynthetic process by transcription from RNA polymerase II promoter(GO:0100032)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates phospholipid biosynthetic process
regulation of fungal-type cell wall biogenesis by transcription from RNA polymerase II promoter(GO:0100033)biological_processAny transcription from RNA polymerase II promoter process that regulates fungal-type cell wall biogenesis
regulation of 4,6-pyruvylated galactose residue biosynthetic process by transcription from RNA polymerase II promoter(GO:0100034)biological_processAny transcription from RNA polymerase II promoter process that regulates 4,6-pyruvylated galactose residue biosynthetic process
obsolete negative regulation of transmembrane transport by transcription from RNA polymerase II promoter(GO:0100035)biological_processOBSOLETE. Any transcription from RNA polymerase II promoter process that negatively_regulates transmembrane transport The term was obsoleted because it is better represented by a GO-CAM model.
positive regulation of purine nucleotide biosynthetic process by transcription from RNA polymerase II promoter(GO:0100036)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates purine nucleotide biosynthetic process
positive regulation of cellular alcohol catabolic process by transcription from RNA polymerase II promoter(GO:0100037)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates cellular alcohol catabolic process
regulation of cellular response to oxidative stress by transcription from RNA polymerase II promoter(GO:0100038)biological_processAny transcription from RNA polymerase II promoter process that regulates cellular response to oxidative stress
regulation of pyrimidine nucleotide biosynthetic process by transcription from RNA polymerase II promoter(GO:0100039)biological_processAny transcription from RNA polymerase II promoter process that regulates pyrimidine nucleotide biosynthetic process
negative regulation of invasive growth in response to glucose limitation by transcription from RNA polymerase II promoter(GO:0100040)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates invasive growth in response to glucose limitation
positive regulation of pseudohyphal growth by transcription from RNA polymerase II promoter(GO:0100041)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates pseudohyphal growth
negative regulation of pseudohyphal growth by transcription from RNA polymerase II promoter(GO:0100042)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates pseudohyphal growth
negative regulation of cellular response to alkaline pH by transcription from RNA polymerase II promoter(GO:0100043)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates cellular response to alkaline pH
negative regulation of cellular hyperosmotic salinity response by transcription from RNA polymerase II promoter(GO:0100044)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates cellular hyperosmotic salinity response
negative regulation of arginine catabolic process by transcription from RNA polymerase II promoter(GO:0100045)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates arginine catabolic process
positive regulation of arginine biosynthetic process by transcription from RNA polymerase II promoter(GO:0100046)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates arginine biosynthetic process
negative regulation of inositol biosynthetic process by transcription from RNA polymerase II promoter(GO:0100047)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates inositol biosynthetic process
positive regulation of phosphatidylcholine biosynthetic process by transcription from RNA polymerase II promoter(GO:0100048)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates phosphatidylcholine biosynthetic process
negative regulation of phosphatidylcholine biosynthetic process by transcription from RNA polymerase II promoter(GO:0100049)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates phosphatidylcholine biosynthetic process
negative regulation of mating type switching by transcription from RNA polymerase II promoter(GO:0100050)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates mating type switching
positive regulation of meiotic nuclear division by transcription from RNA polymerase II promoter(GO:0100051)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates meiotic nuclear division
negative regulation of G1/S transition of mitotic cell cycle by transcription from RNA polymerase II promoter(GO:0100052)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates G1/S transition of mitotic cell cycle
positive regulation of sulfate assimilation by transcription from RNA polymerase II promoter(GO:0100053)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates sulfate assimilation
positive regulation of flocculation via cell wall protein-carbohydrate interaction by transcription from RNA polymerase II promoter(GO:0100054)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates flocculation via cell wall protein-carbohydrate interaction
positive regulation of phosphatidylserine biosynthetic process by transcription from RNA polymerase II promoter(GO:0100055)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates phosphatidylserine biosynthetic process
negative regulation of phosphatidylserine biosynthetic process by transcription from RNA polymerase II promoter(GO:0100056)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates phosphatidylserine biosynthetic process
regulation of phenotypic switching by transcription from RNA polymerase II promoter(GO:0100057)biological_processAny transcription from RNA polymerase II promoter process that regulates phenotypic switching
positive regulation of phenotypic switching by transcription from RNA polymerase II promoter(GO:0100058)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates phenotypic switching
negative regulation of phenotypic switching by transcription from RNA polymerase II promoter(GO:0100059)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates phenotypic switching
obsolete negative regulation of SREBP signaling pathway by transcription factor catabolic process(GO:0100061)biological_processOBSOLETE. Any transcription factor catabolic process process that negatively_regulates SREBP signaling pathway The reason for obsoletion is that this term should be represented by a GO-CAM model.
obsolete positive regulation of SREBP signaling pathway by transcription factor catabolic process(GO:0100062)biological_processOBSOLETE. Any transcription factor catabolic process process that positively_regulates SREBP signaling pathway The reason for obsoletion is that this term should be represented by a GO-CAM model.
obsolete regulation of dipeptide transmembrane transport by transcription from RNA polymerase II promoter(GO:0100063)biological_processOBSOLETE. Any transcription from RNA polymerase II promoter process that regulates dipeptide transmembrane transport The term was obsoleted because it is better represented by a GO-CAM model.
negative regulation of filamentous growth of a population of unicellular organisms in response to starvation by transcription from RNA polymerase II promoter(GO:0100064)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates filamentous growth of a population of unicellular organisms in response to starvation
negative regulation of leucine import by transcription from RNA polymerase II promoter(GO:0100065)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates leucine import
negative regulation of induction of conjugation with cellular fusion by transcription from RNA polymerase II promoter(GO:0100066)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates induction of conjugation with cellular fusion
positive regulation of pyrimidine-containing compound salvage by transcription from RNA polymerase II promoter(GO:0100068)biological_processAny transcription from RNA polymerase II promoter process that positively_regulates pyrimidine-containing compound salvage
negative regulation of neuron apoptotic process by transcription from RNA polymerase II promoter(GO:0100069)biological_processAny transcription from RNA polymerase II promoter process that negatively_regulates neuron apoptotic process
regulation of fatty acid biosynthetic process by transcription from RNA polymerase II promoter(GO:0100070)biological_processAny transcription from RNA polymerase II promoter process that regulates fatty acid biosynthetic process
negative regulation of transcription from RNA polymerase II promoter in response to salt stress(GO:0101007)biological_processAny process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under salt stress. The stress is usually an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
negative regulation of transcription from RNA polymerase II promoter in response to increased salt(GO:0101008)biological_processAny process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of detection of, or exposure to, an increase in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
MBF transcription complex assembly(GO:0120185)biological_processThe aggregation, arrangement and bonding together of a set of components to form an MBF transcription complex.
negative regulation of termination of RNA polymerase II transcription(GO:0120191)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of termination of RNA polymerase II transcription.
obsolete regulation of transcription from RNA polymerase II promoter involved in calcium-mediated signaling(GO:1900031)biological_processOBSOLETE. Any regulation of transcription from RNA polymerase II promoter that is involved in calcium-mediated signaling. This term was made obsolete because regulation of transcription by the signaling pathway is better represented by GO:1900621.
regulation of transcription from RNA polymerase II promoter by calcium-mediated signaling(GO:1900621)biological_processCalcium-mediated signaling that results in regulation of transcription from an RNA polymerase II promoter.
obsolete positive regulation of transcription from RNA polymerase II promoter involved in calcium-mediated signaling(GO:1900061)biological_processOBSOLETE. Any positive regulation of transcription from RNA polymerase II promoter that is involved in calcium-mediated signaling. This term was made obsolete because activation of transcription by the signaling pathway is better represented by GO:1900622.
positive regulation of transcription from RNA polymerase II promoter by calcium-mediated signaling(GO:1900622)biological_processCalcium-mediated signaling that results in positive regulation of transcription from an RNA polymerase II promoter.
regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry(GO:1900094)biological_processAny regulation of transcription from RNA polymerase II promoter that is involved in determination of left/right symmetry.
regulation of reverse transcription(GO:1900268)biological_processAny process that modulates the frequency, rate or extent of reverse transcription.
negative regulation of reverse transcription(GO:1900269)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of reverse transcription.
positive regulation of reverse transcription(GO:1900270)biological_processAny process that activates or increases the frequency, rate or extent of reverse transcription.
positive regulation of mating type switching by regulation of transcription from RNA polymerase II promoter(GO:1900374)biological_processA regulation of transcription from RNA polymerase II promoter that results in positive regulation of mating type switching.
positive regulation of inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter(GO:1900375)biological_processA positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of inositol biosynthetic process.
regulation of thiamine biosynthetic process by regulation of transcription from RNA polymerase II promoter(GO:1900382)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of thiamine biosynthetic process.
negative regulation of cell-cell adhesion by negative regulation of transcription from RNA polymerase II promoter(GO:1900387)biological_processA negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of cell-cell adhesion.
obsolete regulation of vesicle-mediated transport by regulation of transcription from RNA polymerase II promoter(GO:1900388)biological_processOBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in regulation of vesicle-mediated transport. This term was made obsolete because there is no evidence that vesicle-mediated transport is regulated transcriptionally.
regulation of glucose import by regulation of transcription from RNA polymerase II promoter(GO:1900389)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of glucose import.
obsolete regulation of cAMP-mediated signaling by regulation of transcription from RNA polymerase II promoter(GO:1900391)biological_processOBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in regulation of cAMP-mediated signaling. The reason for obsoletion is that cAMP-mediated signaling is not mediated by transcription from RNA polII promoter. See https://github.com/geneontology/go-ontology/issues/14279
regulation of transport by negative regulation of transcription from RNA polymerase II promoter(GO:1900392)biological_processA negative regulation of transcription from RNA polymerase II promoter that results in regulation of transport.
regulation of iron ion transport by regulation of transcription from RNA polymerase II promoter(GO:1900393)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of iron ion transport.
regulation of iron ion import by regulation of transcription from RNA polymerase II promoter(GO:1900400)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of iron ion import.
regulation of carbohydrate metabolic process by regulation of transcription from RNA polymerase II promoter(GO:1900402)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of carbohydrate metabolic process.
negative regulation of cellular amino acid biosynthetic process by negative regulation of transcription from RNA polymerase II promoter(GO:1900403)biological_processA negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of cellular amino acid biosynthetic process.
positive regulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter(GO:1900404)biological_processA positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of DNA repair.
obsolete regulation of cell separation after cytokinesis by regulation of transcription from RNA polymerase II promoter(GO:1900405)biological_processOBSOLETE A regulation of transcription from RNA polymerase II promoter that results in regulation of cell separation after cytokinesis.
regulation of conjugation with cellular fusion by regulation of transcription from RNA polymerase II promoter(GO:1900406)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of conjugation with cellular fusion.
obsolete regulation of histone modification by regulation of transcription from RNA polymerase II promoter(GO:1900410)biological_processOBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in regulation of histone modification. This term was obsoleted because it describes a process that does not exist.
obsolete regulation of histone acetylation by regulation of transcription from RNA polymerase II promoter(GO:1900411)biological_processOBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in regulation of histone acetylation. This term was obsoleted because it describes a process that does not exist.
obsolete regulation of histone methylation by regulation of transcription from RNA polymerase II promoter(GO:1900412)biological_processOBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in regulation of histone methylation. This term was obsoleted because it describes a process that does not exist.
positive regulation of phospholipid biosynthetic process by positive regulation of transcription from RNA polymerase II promoter(GO:1900413)biological_processA positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of phospholipid biosynthetic process.
obsolete regulation of cytokinesis by regulation of transcription from RNA polymerase II promoter(GO:1900414)biological_processOBSOLETE A regulation of transcription from RNA polymerase II promoter that results in regulation of cytokinesis.
regulation of fungal-type cell wall biogenesis by regulation of transcription from RNA polymerase II promoter(GO:1900415)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of fungal-type cell wall biogenesis.
regulation of 4,6-pyruvylated galactose residue biosynthetic process by regulation of transcription from RNA polymerase II promoter(GO:1900416)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of 4,6-pyruvylated galactose residue biosynthetic process.
obsolete negative regulation of transmembrane transport by negative regulation of transcription from RNA polymerase II promoter(GO:1900417)biological_processOBSOLETE. A negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of transmembrane transport. The term was obsoleted because it is better represented by a GO-CAM model.
positive regulation of purine nucleotide biosynthetic process by positive regulation of transcription from RNA polymerase II promoter(GO:1900418)biological_processA positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of purine nucleotide biosynthetic process.
positive regulation of cellular alcohol catabolic process by positive regulation of transcription from RNA polymerase II promoter(GO:1900422)biological_processA positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of cellular alcohol catabolic process.
positive regulation of mating type switching by positive regulation of transcription from RNA polymerase II promoter(GO:1900423)biological_processA positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of mating type switching.
regulation of cellular response to oxidative stress by regulation of transcription from RNA polymerase II promoter(GO:1900427)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of cellular response to oxidative stress.
obsolete negative regulation of tRNA transcription from RNA polymerase III promoter(GO:1900446)biological_processOBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of tRNA transcription from RNA polymerase III promoter. The reason for obsoletion is that there is no specific regulator for negatively regulating tRNA transcription which is separable from general negative regulation of transcription from RNA polymerase III.
regulation of pyrimidine nucleotide biosynthetic process by positive regulation of transcription from RNA polymerase II promoter(GO:1900448)biological_processAny process that modulates the frequency, rate or extent of pyrimidine nucleotide biosynthesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
obsolete regulation of invasive growth in response to glucose limitation by regulation of transcription from RNA polymerase II promoter(GO:1900456)biological_processOBSOLETE. Any process that modulates the frequency, rate or extent of invasive growth in response to glucose limitation by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter. This term was obsoleted at the TermGenie Gatekeeper stage.
negative regulation of invasive growth in response to glucose limitation by negative regulation of transcription from RNA polymerase II promoter(GO:1900460)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of invasive growth in response to glucose limitation by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter(GO:1900461)biological_processAny process that activates or increases the frequency, rate or extent of pseudohyphal growth by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of pseudohyphal growth by negative regulation of transcription from RNA polymerase II promoter(GO:1900462)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of pseudohyphal growth by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of cellular response to alkaline pH by negative regulation of transcription from RNA polymerase II promoter(GO:1900463)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of cellular response to alkalinity by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of cellular hyperosmotic salinity response by negative regulation of transcription from RNA polymerase II promoter(GO:1900464)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of cellular hyperosmotic salinity response by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of arginine catabolic process by negative regulation of transcription from RNA polymerase II promoter(GO:1900465)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of cellular arginine catabolic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of arginine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter(GO:1900466)biological_processAny process that activates or increases the frequency, rate or extent of arginine biosynthetic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of inositol biosynthetic process by negative regulation of transcription from RNA polymerase II promoter(GO:1900471)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of inositol biosynthetic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of phosphatidylcholine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter(GO:1900472)biological_processAny process that activates or increases the frequency, rate or extent of phosphatidylcholine biosynthetic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of phosphatidylcholine biosynthetic process by negative regulation of transcription from RNA polymerase II promoter(GO:1900473)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of phosphatidylcholine biosynthetic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of mating type switching by negative regulation of transcription from RNA polymerase II promoter(GO:1900474)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of mating type switching by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter(GO:1900477)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of G1/S transition of mitotic cell cycle by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of sulfate assimilation by positive regulation of transcription from RNA polymerase II promoter(GO:1900478)biological_processAny process that activates or increases the frequency, rate or extent of sulfate assimilation by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of flocculation via cell wall protein-carbohydrate interaction by positive regulation of transcription from RNA polymerase II promoter(GO:1900524)biological_processAny process that activates or increases the frequency, rate or extent of flocculation via cell wall protein-carbohydrate interaction process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of phosphatidylserine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter(GO:1900525)biological_processAny process that activates or increases the frequency, rate or extent of phosphatidylserine biosynthetic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
negative regulation of phosphatidylserine biosynthetic process by negative regulation of transcription from RNA polymerase II promoter(GO:1900526)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of phosphatidylserine biosynthetic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter(GO:1900545)biological_processA regulation of transcription from RNA polymerase II promoter that results in regulation of phenotypic switching.
positive regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter(GO:1900546)biological_processA regulation of transcription from RNA polymerase II promoter that results in positive regulation of phenotypic switching.
negative regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter(GO:1900547)biological_processA regulation of transcription from RNA polymerase II promoter that results in negative regulation of phenotypic switching.
obsolete regulation of transcription from RNA polymerase II promoter during M/G1 transition of mitotic cell cycle(GO:1901037)biological_processOBSOLETE. Any process that regulates transcription such that the target genes are transcribed during the M/G1 transition of the mitotic cell cycle. This term was made obsolete because it does not refer to a real biological process.
regulation of transcription from RNA polymerase II promoter involved in heart development(GO:1901213)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the development of the heart over time.
obsolete negative regulation of transcription from RNA polymerase II promoter involved in heart development(GO:1901225)biological_processOBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of regulation of transcription from RNA polymerase II promoter involved in heart development. This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete positive regulation of transcription from RNA polymerase II promoter involved in heart development(GO:1901226)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of regulation of transcription from RNA polymerase II promoter involved in heart development. This term was obsoleted at the TermGenie Gatekeeper stage.
negative regulation of transcription from RNA polymerase II promoter involved in heart development(GO:1901227)biological_processAny negative regulation of transcription from RNA polymerase II promoter that is involved in heart development.
positive regulation of transcription from RNA polymerase II promoter involved in heart development(GO:1901228)biological_processAny positive regulation of transcription from RNA polymerase II promoter that is involved in heart development.
positive regulation of transcription from RNA polymerase II promoter involved in defense response to fungus(GO:1901244)biological_processAny process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter to protect the cell or organism in response to the presence of a fungus.
regulation of transcription factor catabolic process(GO:1901483)biological_processAny process that modulates the frequency, rate or extent of transcription factor catabolic process.
negative regulation of transcription factor catabolic process(GO:1901484)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of transcription factor catabolic process.
positive regulation of transcription factor catabolic process(GO:1901485)biological_processAny process that activates or increases the frequency, rate or extent of transcription factor catabolic process.
obsolete negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolic process(GO:1901486)biological_processOBSOLETE. Positive regulation of transcription factor catabolism that results in negative regulation of the SREBP signaling pathway. The reason for obsoletion is that this term should be represented by a GO-CAM model.
obsolete negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolic process in response to increased oxygen levels(GO:1901487)biological_processOBSOLETE. Positive regulation of transcription factor catabolism in response to increased oxygen levels, which results in negative regulation of the SREBP signaling pathway. The reason for obsoletion is that this is better captured in a GO-CAM model. See https://github.com/geneontology/go-ontology/issues/14544
obsolete positive regulation of SREBP signaling pathway by negative regulation of transcription factor catabolic process(GO:1901488)biological_processOBSOLETE. Negative regulation of transcription factor catabolism that results in positive regulation of the SREBP signaling pathway. The reason for obsoletion is that this term should be represented by a GO-CAM model.
obsolete positive regulation of SREBP signaling pathway by negative regulation of transcription factor catabolic process in response to decreased oxygen levels(GO:1901489)biological_processOBSOLETE. Negative regulation of transcription factor catabolism in response to decreased oxygen levels, which results in positive regulation of the SREBP signaling pathway. The reason for obsoletion is that this term should be represented by a GO-CAM model.
positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus(GO:1901522)biological_processAny positive regulation of transcription from RNA polymerase II promoter that is involved in cellular response to chemical stimulus.
regulation of telomeric RNA transcription from RNA pol II promoter(GO:1901580)biological_processAny process that modulates the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter.
negative regulation of telomeric RNA transcription from RNA pol II promoter(GO:1901581)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter.
positive regulation of telomeric RNA transcription from RNA pol II promoter(GO:1901582)biological_processAny process that activates or increases the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter.
obsolete regulation of dipeptide transmembrane transport by regulation of transcription from RNA polymerase II promoter(GO:1901718)biological_processOBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in regulation of dipeptide transmembrane transport. The term was obsoleted because it is better represented by a GO-CAM model.
regulation of transcription of nucleolar large rRNA by RNA polymerase I(GO:1901836)biological_processAny process that modulates the frequency, rate or extent of transcription of nuclear large rRNA mediated by RNA polymerase I.
negative regulation of transcription of nucleolar large rRNA by RNA polymerase I(GO:1901837)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of transcription of nuclear large rRNA transcript mediated by RNA polymerase I.
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I(GO:1901838)biological_processAny process that activates or increases the frequency, rate or extent of transcription of nuclear large rRNA mediated by RNA polymerase I.
obsolete regulation of transcription from RNA polymerase II promoter involved in response to osmotic stress(GO:1902032)biological_processOBSOLETE. Any regulation of transcription from RNA polymerase II promoter that is involved in response to osmotic stress. This term was obsoleted at the TermGenie Gatekeeper stage.
regulation of transcription from RNA polymerase II promoter involved in spermatogenesis(GO:1902064)biological_processAny regulation of transcription from RNA polymerase II promoter that is involved in spermatogenesis.
positive regulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium(GO:1902097)biological_processAny positive regulation of transcription from RNA polymerase II promoter that is involved in defense response to Gram-negative bacterium.
regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator(GO:1902162)biological_processAny process that modulates the frequency, rate or extent of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator.
negative regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator(GO:1902163)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator.
positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator(GO:1902164)biological_processAny process that activates or increases the frequency, rate or extent of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator.
negative regulation of filamentous growth of a population of unicellular organisms in response to starvation by negative regulation of transcription from RNA polymerase II promoter(GO:1902352)biological_processA negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of filamentous growth of a population of unicellular organisms in response to starvation.
positive regulation of induction of conjugation with cellular fusion by negative regulation of transcription from RNA polymerase II promoter by pheromones(GO:1902353)biological_processA negative regulation of transcription from RNA polymerase II promoter by pheromones that results in positive regulation of induction of conjugation with cellular fusion.
negative regulation of leucine import by regulation of transcription from RNA polymerase II promoter(GO:1902574)biological_processA regulation of transcription from RNA polymerase II promoter that results in negative regulation of leucine import.
negative regulation of induction of conjugation with cellular fusion by negative regulation of transcription from RNA polymerase II promoter(GO:1902625)biological_processA negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of induction of conjugation with cellular fusion.
regulation of pri-miRNA transcription by RNA polymerase II(GO:1902893)biological_processAny process that modulates the frequency, rate or extent of pri-miRNA transcription mediated by RNA polymerase II.
negative regulation of pri-miRNA transcription by RNA polymerase II(GO:1902894)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of pri-miRNA transcription mediated by RNA polymerase II.
positive regulation of pri-miRNA transcription by RNA polymerase II(GO:1902895)biological_processAny process that activates or increases the frequency, rate or extent of pri-miRNA transcription mediated by RNA polymerase II.
positive regulation of transcription from RNA polymerase II promoter involved in stress response to cadmium ion(GO:1902901)biological_processAny positive regulation of transcription from RNA polymerase II promoter that is involved in stress response to cadmium ion.
regulation of mitochondrial transcription(GO:1903108)biological_processAny process that modulates the frequency, rate or extent of transcription occuring in the mitochondrion.
positive regulation of mitochondrial transcription(GO:1903109)biological_processAny process that activates or increases the frequency, rate or extent of transcription occuring in the mitochondrion.
obsolete miRNA binding involved in posttranscriptional gene silencing(GO:1903230)molecular_functionOBSOLETE. Any miRNA binding that is involved in posttranscriptional gene silencing. This term was obsoleted at the TermGenie Gatekeeper stage.
mRNA binding involved in posttranscriptional gene silencing(GO:1903231)molecular_functionAny mRNA binding that is involved in posttranscriptional gene silencing.
regulation of transcription initiation from RNA polymerase I promoter(GO:1903357)biological_processAny process that modulates the frequency, rate or extent of transcription initiation from RNA polymerase I promoter.
regulation of nucleic acid-templated transcription(GO:1903506)biological_processAny process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
negative regulation of nucleic acid-templated transcription(GO:1903507)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
positive regulation of nucleic acid-templated transcription(GO:1903508)biological_processAny process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription.
phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in positive regulation of transcription elongation from RNA polymerase II promoter(GO:1903654)biological_processAny phosphorylation of RNA polymerase II C-terminal domain serine 5 residues that is involved in positive regulation of transcription elongation from RNA polymerase II promoter.
phosphorylation of RNA polymerase II C-terminal domain serine 2 residues involved in positive regulation of transcription elongation from RNA polymerase II promoter(GO:1903655)biological_processAny phosphorylation of RNA polymerase II C-terminal domain serine 2 residues that is involved in positive regulation of transcription elongation from RNA polymerase II promoter.
regulation of transcription from RNA polymerase II promoter by histone modification(GO:1903756)biological_processA histone modification that results in regulation of transcription from RNA polymerase II promoter.
positive regulation of transcription from RNA polymerase II promoter by histone modification(GO:1903757)biological_processA histone modification that results in positive regulation of transcription from RNA polymerase II promoter.
negative regulation of transcription from RNA polymerase II promoter by histone modification(GO:1903758)biological_processA histone modification that results in negative regulation of transcription from RNA polymerase II promoter.
positive regulation of pyrimidine-containing compound salvage by positive regulation of transcription from RNA polymerase II promoter(GO:1904001)biological_processA positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of pyrimidine-containing compound salvage.
obsolete negative regulation of transcription from RNA polymerase II promoter involved in negative regulation of neuron apoptotic process(GO:1904079)biological_processOBSOLETE. Any negative regulation of transcription from RNA polymerase II promoter that is involved in negative regulation of neuron apoptotic process. This term was obsoleted at the TermGenie Gatekeeper stage.
positive regulation of transcription from RNA polymerase II promoter involved in neuron fate specification(GO:1904080)biological_processAny positive regulation of transcription from RNA polymerase II promoter that is involved in neuron fate specification.
positive regulation of transcription from RNA polymerase II promoter involved in neuron differentiation(GO:1904081)biological_processAny positive regulation of transcription from RNA polymerase II promoter that is involved in neuron differentiation.
negative regulation of neuron apoptotic process by negative regulation of transcription from RNA polymerase II promoter(GO:1904089)biological_processA negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of neuron apoptotic process.
regulation of transcription by RNA polymerase V(GO:1904279)biological_processAny process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase V.
negative regulation of transcription by RNA polymerase V(GO:1904280)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of transcription mediated by RNA polymerase V.
positive regulation of transcription by RNA polymerase V(GO:1904281)biological_processAny process that activates or increases the frequency, rate or extent of transcription mediated by RNA polymerase V.
negative regulation of ncRNA transcription associated with protein coding gene TSS/TES(GO:1904388)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of ncRNA transcription associated with protein coding gene TSS/TES.
regulation of reactive oxygen species metabolic process by positive regulation of transcription from RNA polymerase II promoter(GO:1904488)biological_processA positive regulation of transcription from RNA polymerase II promoter that results in regulation of reactive oxygen species metabolic process.
regulation of reactive oxygen species metabolic process by negative regulation of transcription from RNA polymerase II promoter(GO:1904489)biological_processA negative regulation of transcription from RNA polymerase II promoter that results in regulation of reactive oxygen species metabolic process.
negative regulation of mitochondrial unfolded protein response by negative regulation of transcription from RNA polymerase II promoter(GO:1904490)biological_processA negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of mitochondrial unfolded protein response.
regulation of chromatin-mediated maintenance of transcription(GO:1904499)biological_processAny process that modulates the frequency, rate or extent of chromatin-mediated maintenance of transcription.
negative regulation of chromatin-mediated maintenance of transcription(GO:1904500)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of chromatin-mediated maintenance of transcription.
positive regulation of chromatin-mediated maintenance of transcription(GO:1904501)biological_processAny process that activates or increases the frequency, rate or extent of chromatin-mediated maintenance of transcription.
regulation of termination of RNA polymerase II transcription(GO:1904594)biological_processAny process that modulates the frequency, rate or extent of termination of RNA polymerase II transcription.
positive regulation of termination of RNA polymerase II transcription(GO:1904595)biological_processAny process that activates or increases the frequency, rate or extent of termination of RNA polymerase II transcription.
obsolete TFIIB-class transcription factor binding involved in negative regulation of transcription(GO:1904725)molecular_functionOBSOLETE. Any TFIIB-class transcription factor binding that is involved in negative regulation of DNA-templated transcription. The reason for obsoletion is that this term represent a GO-CAM model.
regulation of synapse organization by posttranscriptional regulation of gene expression(GO:1904739)biological_processA posttranscriptional regulation of gene expression that results in regulation of synapse organization.
positive regulation of filamentous growth of a population of unicellular organisms in response to starvation by transcription from RNA polymerase II promoter(GO:1904740)biological_processA transcription from RNA polymerase II promoter that results in positive regulation of filamentous growth of a population of unicellular organisms in response to starvation.
positive regulation of filamentous growth of a population of unicellular organisms in response to starvation by positive regulation of transcription from RNA polymerase II promoter(GO:1904741)biological_processA positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of filamentous growth of a population of unicellular organisms in response to starvation.
positive regulation of transcription from RNA polymerase II promoter in response to maltose(GO:1904765)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a maltose stimulus.
positive regulation of induction of conjugation with cellular fusion by regulation of transcription from RNA polymerase II promoter(GO:1904788)biological_processA regulation of transcription from RNA polymerase II promoter that results in positive regulation of induction of conjugation with cellular fusion.
regulation of RNA binding transcription factor activity(GO:1905255)biological_processAny process that modulates the frequency, rate or extent of RNA binding transcription factor activity.
negative regulation of RNA binding transcription factor activity(GO:1905256)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of RNA binding transcription factor activity.
positive regulation of RNA binding transcription factor activity(GO:1905257)biological_processAny process that activates or increases the frequency, rate or extent of RNA binding transcription factor activity.
regulation of snRNA transcription by RNA polymerase II(GO:1905380)biological_processAny process that modulates the frequency, rate or extent of snRNA transcription mediated by RNA polymerase II.
negative regulation of snRNA transcription by RNA polymerase II(GO:1905381)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of snRNA transcription mediated by RNA polymerase II.
positive regulation of snRNA transcription by RNA polymerase II(GO:1905382)biological_processAny process that activates or increases the frequency, rate or extent of snRNA transcription mediated by RNA polymerase II.
obsolete regulation of ferrichrome biosynthetic process by negative regulation of transcription from RNA polymerase II promoter in response to iron(GO:1905525)biological_processOBSOLETE. A negative regulation of transcription from RNA polymerase II promoter in response to iron that results in regulation of ferrichrome biosynthetic process. This term was made obsolete because it was added in error.
obsolete negative regulation of regulation of ferrichrome biosynthetic process by negative regulation of transcription from RNA polymerase II promoter in response to iron(GO:1905545)biological_processOBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of regulation of ferrichrome biosynthetic process by negative regulation of transcription from RNA polymerase II promoter in response to iron. This term was obsoleted at the TermGenie Gatekeeper stage.
positive regulation of transcription from RNA polymerase II promoter in response to reactive oxygen species(GO:1990095)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
positive regulation of transcription from RNA polymerase II promoter in response to superoxide(GO:1990096)biological_processAny process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.
positive regulation by symbiont of host transcription(GO:1990216)biological_processAny process in which an organism activates, maintains or increases the frequency, rate or extent of transcription in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
regulation of transcription from RNA polymerase II promoter in response to DNA damage(GO:1990248)biological_processAny process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of DNA damage.
transcription-coupled nucleotide-excision repair, DNA damage recognition complex(GO:1990250)cellular_componentA protein complex that is capable of identifying lesions in DNA on the actively transcribed strand of the DNA duplex as well as a small subset of lesions not recognized by the general nucleotide-excision repair pathway. The wide range of substrate specificity suggests that the repair complex recognizes distortions in the DNA helix. It subsequently recruits a nucleotide-excision repair, preincision complex.
negative regulation of transcription from RNA polymerase II promoter by transcription factor localization involved in response to DNA damage checkpoint signaling(GO:1990260)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter using a mechanism that involves the localization of a transcription factor and initiated in response to the DNA damage checkpoint signaling.
obsolete positive regulation of MBF transcription factor activity(GO:1990278)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of activity of the transcription factor MBF. This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete negative regulation of MBF transcription factor activity(GO:1990279)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor MBF. This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete negative regulation of G1/S transition of mitotic cell cycle by positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation(GO:1990376)biological_processA positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation that results in negative regulation of mitotic G1/S transition. This term was made obsolete because it would not be used for annotation.
CSL-Notch-Mastermind transcription factor complex(GO:1990433)cellular_componentA DNA-binding transcription factor complex consisting of CSL and mastermind proteins in complex with the cleaved, intracellular domain of Notch. It is required for both repression and activation of Notch target genes.
positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress(GO:1990440)biological_processAny process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an endoplasmic reticulum stress.
negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress(GO:1990441)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an endoplasmic reticulum stress.
CLOCK-BMAL transcription complex(GO:1990513)cellular_componentTranscription factor complex which interacts with E-box regulatory elements in target genes, including Period (Per1, Per2, Per3) and Cryptochrome (Cry1, Cry2), to activate their transcription during the daytime. The CRY-PER complexes inhibit CLOCK-BMAL1-driven transcription in a negative feedback loop to generate circadian rhythms.
regulation of transcription from RNA polymerase II promoter in response to copper ion starvation(GO:1990561)biological_processModulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is deprived of copper ions.
ATF4-CREB1 transcription factor complex(GO:1990589)cellular_componentTranscription factor complex consisting of ATF4 and CREB1 subunits that is capable of binding to cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3') as part of the positive regulation of transcription. Regulatory targets include the GRP78 (HSPA5) promoter in humans, whose activation by this complex is part of the ER stress response pathway.
ATF1-ATF4 transcription factor complex(GO:1990590)cellular_componentTranscription factor complex consisting of ATF1 and ATF4 subunits that is capable of binding to cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3') of the GRP78 (HSPA5) promoter. Involved in the ER stress response pathway.
obsolete positive regulation of pyrimidine-containing compound salvage by positive regulation of transcription from RNA polymerase II promoter(GO:1990652)biological_processOBSOLETE. A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of pyrimidine-containing compound salvage. This term was obsoleted at the TermGenie Gatekeeper stage.
negative regulation of hh target transcription factor activity(GO:1990787)biological_processAny process that decreases the activity of a transcription factor that activates transcription of Hedgehog-target genes in response to Smoothened signaling. In Drosophila, Cubitus interruptus (Ci) is the only identified transcription factor so far in the Hedgehog signaling pathway. In vertebrates members of the Gli protein family are activated by Hedgehog signaling.
negative regulation of sterol import by negative regulation of transcription from RNA polymerase II promoter(GO:1990872)biological_processAny process that decreases the frequency, rate or extent of sterol import, by down regulation of transcription from an RNA polymerase II promoter.
obsolete negative regulation of transcription from RNA polymerase II promoter in response to DNA damage(GO:1990881)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of DNA damage. This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete positive regulation of induction of conjugation with cellular fusion by regulation of transcription from RNA polymerase II promoter(GO:1990894)biological_processOBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in positive regulation of induction of conjugation with cellular fusion. This term was obsoleted during the TG review process. It should have been created using a template.
modulation by host of viral RNA-binding transcription factor activity(GO:1990969)biological_processA process in which a host organism modulates the frequency, rate or extent of the activity of a viral RNA-binding transcription factor.
regulation of DNA-templated transcription, initiation(GO:2000142)biological_processAny process that modulates the frequency, rate or extent of DNA-templated transcription initiation.
negative regulation of DNA-templated transcription, initiation(GO:2000143)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of DNA-templated transcription initiation.
positive regulation of DNA-templated transcription, initiation(GO:2000144)biological_processAny process that activates or increases the frequency, rate or extent of DNA-templated transcription initiation.
obsolete negative regulation of regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor(GO:2000190)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor. This term was made obsolete because it makes no sense and was added in error.
regulation of nuclear receptor transcription coactivator activity(GO:2000325)biological_processAny process that modulates the frequency, rate or extent of ligand-dependent nuclear receptor transcription coactivator activity.
negative regulation of nuclear receptor transcription coactivator activity(GO:2000326)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of ligand-dependent nuclear receptor transcription coactivator activity.
positive regulation of nuclear receptor transcription coactivator activity(GO:2000327)biological_processAny process that activates or increases the frequency, rate or extent of ligand-dependent nuclear receptor transcription coactivator activity.
regulation of fatty acid biosynthetic process by regulation of transcription from RNA polymerase II promoter(GO:2000531)biological_processAny process that modulates the frequency, rate or extent of the biosynthesis of fatty acids, by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter.
regulation of transcription regulatory region DNA binding(GO:2000677)biological_processAny process that modulates the frequency, rate or extent of transcription regulatory region DNA binding.
negative regulation of transcription regulatory region DNA binding(GO:2000678)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of transcription regulatory region DNA binding.
positive regulation of transcription regulatory region DNA binding(GO:2000679)biological_processAny process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding.
positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation(GO:2000721)biological_processAny positive regulation of transcription from RNA polymerase II promoter that is involved in smooth muscle cell differentiation.
regulation of termination of RNA polymerase I transcription(GO:2000730)biological_processAny process that modulates the frequency, rate or extent of termination of RNA polymerase I transcription.
negative regulation of termination of RNA polymerase I transcription(GO:2000731)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of termination of RNA polymerase I transcription.
positive regulation of termination of RNA polymerase I transcription(GO:2000732)biological_processAny process that activates or increases the frequency, rate or extent of termination of RNA polymerase I transcription.
obsolete positive regulation of transcription from RNA polymerase III promoter involved in smooth muscle cell differentiation(GO:2000745)biological_processOBSOLETE. Any positive regulation of transcription from RNA polymerase III promoter that is involved in smooth muscle cell differentiation. This term was made obsolete because it was added in error.
positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process(GO:2000763)biological_processAny positive regulation of transcription from RNA polymerase II promoter that is involved in norepinephrine biosynthetic process.
regulation of termination of RNA polymerase II transcription, poly(A)-coupled(GO:2000804)biological_processAny process that modulates the frequency, rate or extent of termination of RNA polymerase II transcription, poly(A)-coupled.
negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled(GO:2000805)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of termination of RNA polymerase II transcription, poly(A)-coupled.
positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled(GO:2000806)biological_processAny process that activates or increases the frequency, rate or extent of termination of RNA polymerase II transcription, poly(A)-coupled.
negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation(GO:2000820)biological_processAny negative regulation of transcription from RNA polymerase II promoter that is involved in smooth muscle cell differentiation.
obsolete regulation of transcription from RNA polymerase II promoter involved in detection of glucose(GO:2000976)biological_processOBSOLETE. Any regulation of transcription from RNA polymerase II promoter that is involved in detection of glucose. This term was made obolete is that in these terms the 'involved in' process is not truly involved_in (i.e. part_of) the process but instead is causally upstream of it. We advise replacing annotations to these terms with annotations + extensions using the causally_upstream_of relation e.g. P1234 regulation of gene expression [causally_upstream_of] extracellular matrix organization.
regulation of transcription elongation from RNA polymerase I promoter(GO:2001207)biological_processAny process that modulates the frequency, rate or extent of transcription elongation from RNA polymerase I promoter.
negative regulation of transcription elongation by RNA polymerase I(GO:2001208)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of transcription elongation mediated by RNA polymerase I.
positive regulation of transcription elongation from RNA polymerase I promoter(GO:2001209)biological_processAny process that activates or increases the frequency, rate or extent of transcription elongation from RNA polymerase I promoter.
bacterial-type proximal promoter sequence-specific DNA binding(GO:0000986)molecular_functionInteracting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in the proximal promoter of a bacterial gene (or cistron, or operon). The proximal promoter is in cis with and relatively close to the core promoter.
RNA polymerase I activity(GO:0001054)molecular_functionCatalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase I specific promoter to direct initiation and catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
RNA polymerase II activity(GO:0001055)molecular_functionCatalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
RNA polymerase III activity(GO:0001056)molecular_functionCatalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase III specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
RNA polymerase IV activity(GO:0001057)molecular_functionCatalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase IV specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
RNA polymerase V activity(GO:0001058)molecular_functionCatalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase V specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
bacterial-type RNA polymerase holo enzyme binding(GO:0001108)molecular_functionInteracting selectively and non-covalently with the basal transcription machinery which is composed of a bacterial-type RNA polymerase core enzyme and a sigma factor, the minimal set of factors required for formation of the preinitiation complex (PIC) by a bacterial-type RNA polymerase.
bacterial-type RNA polymerase preinitiation complex assembly(GO:0001126)biological_processThe aggregation, arrangement and bonding together of proteins on a bacterial-type RNA polymerase promoter DNA to form the transcriptional preinitiation complex (PIC), required for transcription.
RNA polymerase II complex recruiting activity(GO:0001139)molecular_functionInteracting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way in order to facilitate the aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
mitochondrial RNA polymerase termination site sequence-specific DNA binding(GO:0001145)molecular_functionInteracting selectively and non-covalently with a DNA sequence that controls mitochondrial transcription termination.
RNA polymerase I CORE element sequence-specific DNA binding(GO:0001164)molecular_functionInteracting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery. This site is often referred to as the CORE element. In mammalian cells, the CORE element functions in conjunction with the Upstream Control Element (UCE), while in fungi, protozoa, and plants, the CORE element functions without a UCE.
RNA polymerase I preinitiation complex assembly(GO:0001188)biological_processThe aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase I promoter.
nuclear receptor activity(GO:0004879)molecular_functionCombining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
DNA replication-independent nucleosome assembly(GO:0006336)biological_processThe formation of nucleosomes outside the context of DNA replication.
chromatin silencing(GO:0006342)biological_processRepression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
auxin-activated signaling pathway(GO:0009734)biological_processA series of molecular signals generated by the binding of the plant hormone auxin to a receptor, and ending with modulation of a downstream cellular process, e.g. transcription.
obsolete promoter binding(GO:0010843)molecular_functionOBSOLETE. Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factor complexes of the basal transcription machinery. This term was made obsolete because the word "promoter" is used ambiguously in the literature. It sometimes is used to refer specifically to the "core promoter" region recognized by the basal transcription machinery, and other times is used to refer to a larger regulatory region composed of the core promoter and also the regulatory region adjacent (proximal) to the core promoter. The core promoter proximal region is typically recognized by "regulatory transcription factors", such as Gal4 in S. cerevisiae.
RNA interference(GO:0016246)biological_processThe process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.
CCAAT-binding factor complex(GO:0016602)cellular_componentA heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5.
sigma factor activity(GO:0016987)molecular_functionSigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins.
obsolete mRNA splicing via endonucleolytic cleavage and ligation involved in unfolded protein response(GO:0030969)biological_processOBSOLETE. The spliceosome-independent cleavage and ligation of the mRNA encoding a UFP-specific transcription factor to remove a single intron, thereby increasing both the translational efficiency of the processed mRNA and the activity of the protein it encodes. The reason for obsoletion is that this process represent a single MF (single step) of the IRE1-mediated unfolded protein response (GO:0036498).
chromatin silencing by small RNA(GO:0031048)biological_processRepression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region.
SREBP signaling pathway(GO:0032933)biological_processA series of molecular signals from the endoplasmic reticulum to the nucleus generated as a consequence of decreased levels of one or more sterols (and in some yeast, changes in oxygen levels) and which proceeds through activation of a sterol response element binding transcription factor (SREBP) to result in up-regulation of target gene transcription.
FACT complex(GO:0035101)cellular_componentAn abundant nuclear complex, which was originally identified in mammalian systems as a factor required for transcription elongation on chromatin templates. The FACT complex has been shown to destablilize the interaction between the H2A/H2B dimer and the H3/H4 tetramer of the nucleosome, thus reorganizing the structure of the nucleosome. In this way, the FACT complex may play a role in DNA replication and other processes that traverse the chromatin, as well as in transcription elongation. FACT is composed of two proteins that are evolutionarily conserved in all eukaryotes and homologous to mammalian Spt16 and SSRP1. In metazoans, the SSRP1 homolog contains an HMG domain; however in fungi and protists, it does not. For example, in S. cerevisiae the Pob3 protein is homologous to SSRP1, but lacks the HMG chromatin binding domain. Instead, the yFACT complex of Spt16p and Pob3p, binds to nucleosomes where multiple copies of the HMG-domain containing protein Nhp6p have already bound, but Nhp6p does not form a stable complex with the Spt16p/Pob3p heterodimer.
ATF6-mediated unfolded protein response(GO:0036500)biological_processA series of molecular signals mediated by the endoplasmic reticulum membrane stress sensor ATF6 (activating transcription factor 6). Begins with activation of ATF6 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. Under conditions of endoplasmic reticulum stress, ATF6 translocates to the Golgi where it is processed by proteases to release a cytoplasmic domain (ATF6f), which operates as a transcriptional activator of many genes required to restore folding capacity.
nodal signaling pathway involved in determination of left/right asymmetry(GO:0038107)biological_processA series of molecular signals initiated by the binding of a nodal protein to an activin receptor on the surface of a target cell, which contributes to the establishment of an organism's body plan or part of an organism with respect to the left and right halves.
suppression by virus of host STAT activity(GO:0039562)biological_processAny process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT (signal transducer and activator of transcription) activity. STATs are SH2 domain-containing proteins which lie downstream of many signaling receptors. Upon phosphorylation by JAKs, STAT proteins hetero- or homo-dimerize and translocate to the nucleus to activate transcription of target genes.
RNA polymerase II preinitiation complex assembly(GO:0051123)biological_processThe aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
elongin complex(GO:0070449)cellular_componentA transcription elongation factor complex that suppresses RNA polymerase II pausing, and may act by promoting proper alignment of the 3'-end of nascent transcripts with the polymerase catalytic site. Consists of a transcriptionally active Elongin A subunit (abut 100 kDa)and two smaller Elongin B (about 18 kDa) and Elongin C (about 15 kDa)subunits.
SWI/SNF superfamily-type complex(GO:0070603)cellular_componentA protein complex that contains an ortholog of the Saccharomyces ATPase Swi2/Snf2 as one of the catalytic subunit components (ATPase) and mediates assembly of nucleosomes, changes to the spacing or structure of nucleosomes, or some combination of those activities in a manner that requires ATP.
P-TEFb complex(GO:0070691)cellular_componentA dimeric positive transcription elongation factor complex b that comprises a cyclin-dependent kinase containing the catalytic subunit, Cdk9, and a regulatory subunit, cyclin T.
CTDK-1 complex(GO:0070692)cellular_componentA positive transcription elongation factor complex that comprises the CDK kinase CTK1 (in budding yeast), Lsk1 (in fission yeast) (corresponding to the Panther PTHR24056:SF39 family), a cyclin and an additional gamma subunit (corresponding to the InterPRO entry IPR024638).
ISGF3 complex(GO:0070721)cellular_componentA transcription factor complex that consists of a Stat1-Stat2 heterodimer and the IRF9 protein.
RNA polymerase III preinitiation complex assembly(GO:0070898)biological_processThe aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase III promoter.
cap snatching(GO:0075526)biological_processA transcription initiation process during which a nucleotide sequence between 10 and 20 nucleotides in size is cleaved from the 5' end of host mRNAs by a viral RNA-dependent polymerase. The capped leader sequence obtained is subsequently used to prime transcription on the viral genome, which ultimately leads to the synthesis of capped, translatable viral mRNAs.
viral RNA editing(GO:0075527)biological_processThe process by which bases in viral mRNA are chemically altered during viral transcription. This is usually the incorporation of 1 - 6 additional nucleotides, which shifts the reading frame, allowing the generation of different protein products or through a specific nucleotide change that eliminates the termination codon.
STAT family protein binding(GO:0097677)molecular_functionInteracting selectively and non-covalently with any member of the signal transducers and activators of transcription (STAT) protein family. STATs are, as the name indicates, both signal transducers and transcription factors. STATs are activated by cytokines and some growth factors and thus control important biological processes including cell growth, cell differentiation, apoptosis and immune responses.
regulation of RNA interference(GO:1900368)biological_processAny process that modulates the frequency, rate or extent of RNA interference.
negative regulation of RNA interference(GO:1900369)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of RNA interference.
positive regulation of RNA interference(GO:1900370)biological_processAny process that activates or increases the frequency, rate or extent of RNA interference.
obsolete negative regulation of SREBP signaling pathway by negative regulation of DNA binding(GO:1901294)biological_processOBSOLETE. Negative regulation of DNA binding that results in negative regulation of a SREBP signaling pathway. The reason for obsoletion is that this term should be represented by a GO-CAM model.
conversion of ds siRNA to ss siRNA involved in chromatin silencing by small RNA(GO:1902360)biological_processAny conversion of ds siRNA to ss siRNA that is involved in chromatin silencing by small RNA.
RNA interference involved in olfactory learning(GO:1903453)biological_processAny RNA interference that is involved in olfactory learning.
regulation of RNA polymerase III activity(GO:1903622)biological_processAny process that modulates the frequency, rate or extent of RNA polymerase III activity.
negative regulation of RNA polymerase III activity(GO:1903623)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of RNA polymerase III activity.
regulation of ATF6-mediated unfolded protein response(GO:1903891)biological_processAny process that modulates the frequency, rate or extent of the ATF6-mediated unfolded protein response.
negative regulation of ATF6-mediated unfolded protein response(GO:1903892)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of the ATF6-mediated unfolded protein response.
positive regulation of ATF6-mediated unfolded protein response(GO:1903893)biological_processAny process that activates or increases the frequency, rate or extent of the ATF6-mediated unfolded protein response.
FACT complex assembly(GO:1905635)biological_processThe aggregation, arrangement and bonding together of a set of components to form a FACT complex.
regulation of FACT complex assembly(GO:1905644)biological_processAny process that modulates the frequency, rate or extent of FACT complex assembly.
negative regulation of FACT complex assembly(GO:1905645)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of FACT complex assembly.
positive regulation of FACT complex assembly(GO:1905646)biological_processAny process that activates or increases the frequency, rate or extent of FACT complex assembly.
C/EBP complex(GO:1990647)cellular_componentA dimeric, sequence specific DNA-binding transcription factor complex regulating the expression of genes involved in immune and inflammatory responses. Exists at least as alpha and beta homodimeric forms. Binds to regulatory regions of several acute-phase and cytokines genes and probably plays a role in the regulation of acute-phase reaction, inflammation and hemopoiesis. The consensus recognition site is 5'-T[TG]NNGNAA[TG]-3'. Transcription factor activity is inhibited by binding of CHOP forming heterodimers with alternative transcription factor activities.
G1/S transition of mitotic cell cycle(GO:0000082)biological_processThe mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
SAGA complex(GO:0000124)cellular_componentA SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery; the ubiquitin specifc protease Ubp-8.
PCAF complex(GO:0000125)cellular_componentA large multiprotein complex that possesses histone acetyltransferase activity and is involved in regulation of transcription. The composition is similar to that of the SAGA complex, but includes fewer Spt and Ada proteins, and more TAFs.
phosphorelay response regulator activity(GO:0000156)molecular_functionResponds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.
chromatin silencing at rDNA(GO:0000183)biological_processRepression of transcription of ribosomal DNA by altering the structure of chromatin.
RNA 7-methylguanosine cap binding(GO:0000340)molecular_functionInteracting selectively and non-covalently with the 7-methylguanosine group added cotranscriptionally to the 5' end of RNA molecules transcribed by polymerase II.
RNA trimethylguanosine cap binding(GO:0000341)molecular_functionInteracting selectively and non-covalently with the trimethylguanosine (m(3)(2,2,7)-GTP) group located at the 5' end of some RNA molecules. Such trimethylated cap structures, generally produced by posttranscriptional modification of a 7-methylguanosine cap, are often found on snRNAs and snoRNAs transcribed by RNA polymerase II, but have also be found on snRNAs transcribed by RNA polymerase III. They have also been found on a subset of the mRNA population in some species, e.g. C. elegans.
THO complex(GO:0000347)cellular_componentThe THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1p, Tho2p, Thp1p, and Mft1p, while the human complex is composed of 7 subunits.
EKC/KEOPS complex(GO:0000408)cellular_componentA protein complex involved in t6A tRNA modification; originally proposed to be involved in transcription as well as promoting telomere uncapping and telomere elongation. For example, in Saccharomyces cerevisiae the complex contains Bud32p, Kae1p, Gon7p, Cgi121p, and Pcc1p.
core TFIIH complex portion of holo TFIIH complex(GO:0000438)cellular_componentThe core TFIIH complex when it is part of the general transcription factor TFIIH.
nucleoplasmic THO complex(GO:0000446)cellular_componentThe THO complex when it is acting as a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. In S. cerevisiae, it is composed of four subunits: Hpr1, Tho2, Thp2, and Mft1, while the human complex is composed of 7 subunits.
snoRNA guided rRNA 2'-O-methylation(GO:0000452)biological_processThe posttranscriptional addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis using a snoRNA guide that targets the position of methylation.
endonucleolytic cleavage in 3'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)(GO:0000471)biological_processEndonucleolytic cleavage within the 3'-External Transcribed Spacer (ETS) of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. In S. cerevisiae, endonucleolytic cleavage within the 3'-ETS of the pre-RNA, which may occur cotranscriptionally, is the first step in rRNA processing, and initiates a cascade of subsequent processing and modification events.
RNA polymerase I upstream activating factor complex(GO:0000500)cellular_componentA complex required for the transcription of rDNA by RNA polymerase I. In yeast the complex consists of Rrrn5p, Rrn9p, Rrn10p, histones H3 and H4, and Uaf30p.
RNA polymerase II regulatory region sequence-specific DNA binding(GO:0000977)molecular_functionInteracting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
RNA polymerase II proximal promoter sequence-specific DNA binding(GO:0000978)molecular_functionInteracting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in the proximal promoter of a gene transcribed by RNA polymerase II. The proximal promoter is in cis with and relatively close to the core promoter.
bacterial-type RNA polymerase regulatory region sequence-specific DNA binding(GO:0000984)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is part of a regulatory region that controls the transcription of a gene or operon by a bacterial-type RNA polymerase.
proximal promoter sequence-specific DNA binding(GO:0000987)molecular_functionInteracting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in the proximal promoter. The proximal promoter is in cis with and relatively close to the core promoter.
polymerase III regulatory region sequence-specific DNA binding(GO:0000992)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is part of a regulatory region that controls transcription by RNA polymerase III. The transcribed region might be contain a single gene or a cistron containing multiple genes.
RNA polymerase III type 1 promoter sequence-specific DNA binding(GO:0001002)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition.
RNA polymerase III type 2 promoter sequence-specific DNA binding(GO:0001003)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs.
RNA polymerase III type 3 promoter sequence-specific DNA binding(GO:0001006)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III (Pol III). A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae.
RNA polymerase II regulatory region DNA binding(GO:0001012)molecular_functionInteracting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
RNA polymerase I regulatory region DNA binding(GO:0001013)molecular_functionInteracting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase I. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
RNA polymerase III regulatory region DNA binding(GO:0001016)molecular_functionInteracting selectively and non-covalently with a DNA region that controls the transcription of a gene by RNA polymerase III. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
bacterial-type RNA polymerase regulatory region DNA binding(GO:0001017)molecular_functionInteracting selectively and non-covalently with a DNA region that controls the transcription of a gene or operon by a bacterial-type RNA polymerase. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
mitochondrial promoter sequence-specific DNA binding(GO:0001018)molecular_functionInteracting selectively and non-covalently with a DNA region that controls the transcription of the mitochondrial DNA.
plastid RNA polymerase regulatory region DNA binding(GO:0001019)molecular_functionInteracting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by a plastid RNA polymerase. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
RNA polymerase III type 1 promoter DNA binding(GO:0001030)molecular_functionInteracting selectively and non-covalently with a region of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition.
RNA polymerase III type 2 promoter DNA binding(GO:0001031)molecular_functionInteracting selectively and non-covalently with a region of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs.
RNA polymerase III type 3 promoter DNA binding(GO:0001032)molecular_functionInteracting selectively and non-covalently with a region of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III. A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae.
RNA polymerase III hybrid type promoter DNA binding(GO:0001037)molecular_functionInteracting selectively and non-covalently with a region of DNA that is a part of a hybrid promoter that controls transcription by RNA polymerase III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene.
RNA polymerase III hybrid type promoter sequence-specific DNA binding(GO:0001039)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is a part of a hybrid type promoter that controls transcription by RNA polymerase III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene.
core promoter sequence-specific DNA binding(GO:0001046)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
core promoter binding(GO:0001047)molecular_functionInteracting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
regulatory region nucleic acid binding(GO:0001067)molecular_functionInteracting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair.
regulatory region RNA binding(GO:0001069)molecular_functionInteracting selectively and non-covalently with a RNA region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair.
promoter clearance from RNA polymerase III promoter(GO:0001110)biological_processAny process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase III, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase.
promoter clearance from RNA polymerase II promoter(GO:0001111)biological_processAny process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase II, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors.
promoter clearance from bacterial-type RNA polymerase promoter(GO:0001122)biological_processAny process involved in the transition from the initiation to the elongation phase of transcription by a bacterial-type RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance generally involves dissociation of the sigma initiation factor.
bacterial-type RNA polymerase enhancer sequence-specific DNA binding(GO:0001150)molecular_functionInteracting selectively and non-covalently with a sequence of DNA that is an enhancer region that helps activate transcription of a gene or operon by a bacterial-type RNA polymerase. Enhancers for sigma-54 holoenzymes are typically located 80 to 150 base pairs upstream from the transcription start site, although they can be further away or may be downstream of the promoter. Some transcription units dependent on sigma-70 holoenzymes may also include enhancer sequences.
enhancer sequence-specific DNA binding(GO:0001158)molecular_functionInteracting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
RNA polymerase I regulatory region sequence-specific DNA binding(GO:0001163)molecular_functionInteracting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase I.
promoter clearance from RNA polymerase I promoter(GO:0001182)biological_processAny process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase I, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors.
promoter clearance from RNA polymerase I promoter for nuclear large rRNA transcript(GO:0001184)biological_processAny process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase I at a promoter for the nuclear large ribosomal RNA (rRNA) transcript, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors.
RNA methylation(GO:0001510)biological_processPosttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor.
pseudouridine synthesis(GO:0001522)biological_processThe intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
fibrillar center(GO:0001650)cellular_componentA structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures.
tRNA 3'-terminal CCA addition(GO:0001680)biological_processPost-transcriptional addition of the terminal 3' CCA sequence to a tRNA which does not encode this sequence within the primary transcript. CCA addition proceeds by the sequential addition of CTP, CTP, and then ATP to the 3' end of the tRNA, yielding a diphosphate with each nucleotide addition.
tRNA wobble base modification(GO:0002097)biological_processThe process in which the nucleotide at position 34 in the anticodon of a tRNA is post-transcriptionally modified.
tRNA wobble uridine modification(GO:0002098)biological_processThe process in which a uridine in position 34 of a tRNA is post-transcriptionally modified.
tRNA wobble guanine modification(GO:0002099)biological_processThe process in which a guanine in t position 34 of a tRNA is post-transcriptionally modified.
tRNA wobble adenosine to inosine editing(GO:0002100)biological_processThe process in which an adenosine in position 34 of a tRNA is post-transcriptionally converted to inosine.
tRNA wobble cytosine modification(GO:0002101)biological_processThe process in which a cytosine in position 34 of a tRNA is post-transcriptionally modified.
generation of mature 3'-end of 5S rRNA generated by RNA polymerase III(GO:0002107)biological_processThe removal of extra uridine residues from the 3' end of a 5S pre-rRNA generated by transcription by RNA polymerase III to generate the mature 3'-end.
tRNA wobble base cytosine methylation(GO:0002127)biological_processThe process in which the base of cytosine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the C5 position.
wobble position guanine ribose methylation(GO:0002129)biological_processThe process in which the ribose of guanosine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position.
wobble position ribose methylation(GO:0002130)biological_processThe process in which the ribose base of the nucleotide at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'O position.
wobble position cytosine ribose methylation(GO:0002131)biological_processThe process in which the ribose of cytidine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position.
wobble position uridine ribose methylation(GO:0002132)biological_processThe process in which the ribose of uridine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position.
tRNA wobble base lysidine biosynthesis(GO:0002136)biological_processThe process in which the carbonyl of cytosine at position 34 of a tRNA is post-transcriptionally replaced by lysine.
tRNA wobble position uridine thiolation(GO:0002143)biological_processThe process in which a uridine residue at position 34 in the anticodon of a tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from cysteine to position C2 by several steps.
steroid receptor RNA activator RNA binding(GO:0002153)molecular_functionInteracting selectively and non-covalently with the steroid receptor RNA activator RNA (SRA). SRA enhances steroid hormone receptor transcriptional activity as an RNA transcript by an indirect mechanism that does not involve SRA-steroid receptor binding.
MAML1-RBP-Jkappa- ICN1 complex(GO:0002193)cellular_componentA protein complex that consists of the intracellular domain of Notch1 (ICN1), the DNA-binding transcription factor RBP-Jkappa, and the transcriptional coactivator Mastermind-like-1 (MAML1); the complex is involved in transcriptional activation in response to Notch-mediated signaling.
MECO complex(GO:0002929)cellular_componentA highly stable complex composed of the ATAC complex and the mediator complex (also called TRAP or MED). MECO binds and regulates the transcription of a subset of non-coding RNAs transcribed by RNA polymerase II.
sphingosine-1-phosphate receptor signaling pathway(GO:0003376)biological_processA series of molecular signals initiated by the sphingolipid sphingosine-1-phosphate (S1P) binding to a receptor on the surface of the cell, and which proceeds with the activated receptor transmitting the signal by promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
steroid hormone receptor activity(GO:0003707)molecular_functionCombining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
retinoic acid receptor activity(GO:0003708)molecular_functionCombining with retinoic acid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. Retinoic acid is one of the forms of vitamin A.
JUN kinase activity(GO:0004705)molecular_functionCatalysis of the reaction: JUN + ATP = JUN phosphate + ADP. This reaction is the phosphorylation and activation of members of the JUN family, a gene family that encodes nuclear transcription factors.
aryl hydrocarbon receptor activity(GO:0004874)molecular_functionCombining with an aryl hydrocarbon and transmitting the signal to initiate a change in cell activity. The aryl hydrocarbon receptor is a ligand-activated transcription factor which translocates to the nucleus to activate transcription upon ligand-binding.
juvenile hormone receptor activity(GO:0004880)molecular_functionCombining with juvenile hormone and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
androgen receptor activity(GO:0004882)molecular_functionCombining with an androgen and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with an androgen response element in DNA in order to modulate transcription by RNA polymerase II.
glucocorticoid receptor activity(GO:0004883)molecular_functionCombining with a glucocorticoid and transmitting the signal within the cell trigger a change in cell activity or function.
ecdysteroid hormone receptor activity(GO:0004884)molecular_functionCombining with an ecdysteroid hormone and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
9-cis retinoic acid receptor activity(GO:0004886)molecular_functionCombining with 9-cis retinoic acid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
thyroid hormone receptor activity(GO:0004887)molecular_functionCombining with thyroid hormone and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
signal transduction(GO:0007165)biological_processThe cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
transmembrane receptor protein tyrosine kinase signaling pathway(GO:0007169)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
transmembrane receptor protein serine/threonine kinase signaling pathway(GO:0007178)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
transforming growth factor beta receptor, common-partner cytoplasmic mediator activity(GO:0030616)molecular_functionA TGF-beta cytoplasmic mediator that forms a complex with a phosphorylated pathway-specific mediator. The heterocomplex translocates to the nucleus to regulate transcription.
transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity(GO:0030618)molecular_functionA TGF-beta cytoplasmic mediator that is phosphorylated by a TGFbeta receptor and complexes with a common-partner mediator. The- heterocomplex translocates to the nucleus to regulate transcription.
RNA modification guide activity(GO:0030555)molecular_functionSpecifies the site of a posttranscriptional modification in an RNA molecule by base pairing with a short sequence around the target residue.
chromatin silencing complex(GO:0005677)cellular_componentAny protein complex that mediates changes in chromatin structure that result in transcriptional silencing.
polytene chromosome puff(GO:0005703)cellular_componentA swelling at a site along the length of a polytene chromosome, thought to be the site of active transcription.
nuclear euchromatin(GO:0005719)cellular_componentThe dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.
nucleolus(GO:0005730)cellular_componentA small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
obsolete short patch mismatch repair system(GO:0006299)biological_processOBSOLETE. The repair of mismatched DNA where the gap to be repaired is only one nucleotide. DNA polymerase is the preferred polymerase in short patch repair, performing gap filling DNA synthesis and removal of the 5'-deoxyribose phosphate of the abasic site. This term was made obsolete because 'short patch' is a relative statement, often used ambiguously, and does not necessarily represent a process; the processes it can stand for are base excision repair, nucleotide excision repair, transcription-coupled nucleotide excision repair, and mismatch repair.
chromatin remodeling(GO:0006338)biological_processDynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
chromatin insulator sequence binding(GO:0043035)molecular_functionInteracting selectively and non-covalently and stoichiometrically with a chromatin insulator sequence, a DNA sequence that prevents enhancer-mediated activation or repression of transcription.
establishment of chromatin silencing(GO:0006343)biological_processThe initial formation of a transcriptionally silent chromatin structure such as heterochromatin.
maintenance of chromatin silencing(GO:0006344)biological_processThe maintenance of chromatin in a transcriptionally silent state such as heterochromatin.
methylation-dependent chromatin silencing(GO:0006346)biological_processRepression of transcription by methylation of DNA, leading to the formation of heterochromatin.
chromatin silencing at telomere(GO:0006348)biological_processRepression of transcription of telomeric DNA by altering the structure of chromatin.
obsolete activation of SoxR protein(GO:0006981)biological_processOBSOLETE The conversion of the SoxR transcription factor to its active (oxidized) form. This term was made obsolete because it was too specific with respect to a single gene product.
ER overload response(GO:0006983)biological_processThe series of molecular signals generated by the accumulation of normal or misfolded proteins in the endoplasmic reticulum and leading to activation of transcription by NF-kappaB.
ER-nucleus signaling pathway(GO:0006984)biological_processAny series of molecular signals that conveys information from the endoplasmic reticulum to the nucleus, usually resulting in a change in transcriptional regulation.
IRE1-mediated unfolded protein response(GO:0036498)biological_processA series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
traversing start control point of mitotic cell cycle(GO:0007089)biological_processA cell cycle process by which a cell commits to entering S phase via a positive feedback mechanism between the regulation of transcription and G1 CDK activity.
cell surface receptor signaling pathway(GO:0007166)biological_processA series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
enzyme linked receptor protein signaling pathway(GO:0007167)biological_processAny series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription.
receptor guanylyl cyclase signaling pathway(GO:0007168)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses guanylyl cyclase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
epidermal growth factor receptor signaling pathway(GO:0007173)biological_processA series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
transforming growth factor beta receptor signaling pathway(GO:0007179)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
transmembrane receptor protein tyrosine phosphatase signaling pathway(GO:0007185)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses protein tyrosine phosphatase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
G protein-coupled receptor signaling pathway(GO:0007186)biological_processA series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
G protein-coupled acetylcholine receptor signaling pathway(GO:0007213)biological_processAny series of molecular signals initiated by an acetylcholine receptor on the surface of the target cell binding to one of its physiological ligands, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction and ends with regulation of a downstream cellular process, e.g. transcription.
glutamate receptor signaling pathway(GO:0007215)biological_processA series of molecular signals initiated by the binding of glutamate to a glutamate receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
G protein-coupled glutamate receptor signaling pathway(GO:0007216)biological_processA series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. Ends with regulation of a downstream cellular process, e.g. transcription.
Notch signaling pathway(GO:0007219)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
integrin-mediated signaling pathway(GO:0007229)biological_processA series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
I-kappaB kinase/NF-kappaB signaling(GO:0007249)biological_processThe process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
I-kappaB phosphorylation(GO:0007252)biological_processThe process of introducing a phosphate group into an inhibitor of kappa B (I-kappaB) protein. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing bound NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
cytoplasmic sequestering of NF-kappaB(GO:0007253)biological_processThe selective interaction of the transcription factor NF-kappaB with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus.
JAK-STAT cascade(GO:0007259)biological_processAny process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The JAK-STAT cascade begins with activation of STAT proteins by members of the JAK family of tyrosine kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins.
tyrosine phosphorylation of STAT protein(GO:0007260)biological_processThe process of introducing a phosphate group to a tyrosine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
obsolete JAK-induced STAT protein dimerization(GO:0007261)biological_processOBSOLETE. The formation of a dimer of two STAT proteins (Signal Transducers and Activators of Transcription) following their activation by members of the janus activated kinase (JAK) family of tyrosine kinases. This term was made obsolete because it is ambiguous, and protein dimerization is represented by molecular function terms.
regulation of rhodopsin gene expression(GO:0007468)biological_processAny process that modulates the frequency, rate or extent of rhodopsin gene expression. This includes transcriptional, translational, or posttranslational regulation.
chromatin silencing at silent mating-type cassette(GO:0030466)biological_processRepression of transcription at silent mating-type loci by alteration of the structure of chromatin.
long-term memory(GO:0007616)biological_processThe memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
Toll signaling pathway(GO:0008063)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to the receptor Toll on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
decapentaplegic signaling pathway(GO:0008101)biological_processA series of molecular signals initiated by the binding of decapentaplegic (dpp) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
RNA guanylyltransferase activity(GO:0008192)molecular_functionCatalysis of the posttranscriptional addition of a guanyl residue to the 5' end of an RNA molecule.
tRNA guanylyltransferase activity(GO:0008193)molecular_functionCatalysis of the posttranscriptional addition of a guanyl residue to the 5' end of a tRNA molecule; observed for His tRNAs.
ecdysone receptor holocomplex(GO:0008230)cellular_componentA heterodimeric complex containing the products of the insect genes Ecdysone receptor (EcR) and ultraspiracle (usp). Binding of ecdysone promotes association between the two subunits, and the receptor complex then initiates molting and metamorphosis by binding DNA and regulating the transcription of target genes.
repressor ecdysone receptor complex(GO:0008231)cellular_componentA protein complex consisting of a heterodimer of Ecdysone receptor (EcR) and ultraspiracle (usp) plus an associated corepressor such as SMRTER, which represses transcription of target genes.
activator ecdysone receptor complex(GO:0008232)cellular_componentA protein complex consisting of a heterodimer of Ecdysone receptor (EcR) and ultraspiracle (usp) bound to the ligand ecdysone, which activates transcription of target genes.
torso signaling pathway(GO:0008293)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to torso (a receptor tyrosine kinase) on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
IkappaB kinase complex(GO:0008385)cellular_componentA trimeric protein complex that phosphorylates inhibitory-kappaB (I-kappaB) proteins. The complex is composed of two kinase subunits (alpha and beta) and a regulatory gamma subunit (also called NEMO). In a resting state, NF-kappaB dimers are bound to inhibitory IKB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity(GO:0008413)molecular_functionCatalysis of the reaction: 8-oxo-7,8-dihydroguanosine triphosphate = 8-oxo-7,8-dihydroguanosine phosphate + diphosphate. 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for transcription.
calcitriol receptor activity(GO:0008434)molecular_functionCombining with calcitriol, the hormonally active form of vitamin D3, and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
CHRAC(GO:0008623)cellular_componentAn ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals, Isw2 in S. cerevisiae), an ACF1 homolog, and additional small histone fold subunits (generally two of these, but Xenopus has only one and some additional non-conserved subunits). CHRAC plays roles in the regulation of RNA polymerase II transcription and in DNA replication and repair.
obsolete negative regulation of survival gene product expression(GO:0008634)biological_processOBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of survival gene product expression; survival gene products are those that antagonize the apoptotic program. Regulation can be at the transcriptional, translational, or posttranslational level. This term was made obsolete because the meaning of the term is ambiguous: the same gene product may or may not have a role in apoptosis depending on the cell type, tissue type, condition, etc.
translational attenuation(GO:0009386)biological_processTranslational attenuation is a regulatory mechanism analogous to ribosome-mediated transcriptional attenuation. The system requires the presence of a short ORF, called a leader peptide, encoded in the mRNA upstream of the ribosome-binding site and start codon of the gene whose translation is to be regulated. Certain conditions, such as presence of the antibiotic tetracycline in bacteria or amino acid starvation, may cause slowing or stalling of the ribosome translating the leader peptide. The stalled ribosome masks a region of the mRNA and affects which of two alternative mRNA folded structures will form, therefore controlling whether or not a ribosome will bind and initiate translation of the downstream gene. Translational attenuation is analogous to ribosome-mediated transcriptional attenuation, in which mRNA remodeling caused by ribosome stalling regulates transcriptional termination rather than translational initiation.
virus induced gene silencing(GO:0009616)biological_processSpecific posttranscriptional gene inactivation ('silencing') both of viral gene(s), and host gene(s) homologous to the viral genes. This silencing is triggered by viral infection, and occurs through a specific decrease in the level of mRNA of both host and viral genes.
cytokinin-activated signaling pathway(GO:0009736)biological_processA series of molecular signals generated by the binding of a cytokinin to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
abscisic acid-activated signaling pathway(GO:0009738)biological_processA series of molecular signals generated by the binding of the plant hormone abscisic acid (ABA) to a receptor, and ending with modulation of a cellular process, e.g. transcription.
ethylene-activated signaling pathway(GO:0009873)biological_processA series of molecular signals generated by the reception of ethylene (ethene, C2H4) by a receptor and ending with modulation of a cellular process, e.g. transcription.
obsolete microRNA metabolic process(GO:0010194)biological_processOBSOLETE. The chemical reactions and pathways involving microRNA, a large family of 21-22 nucleotide non-coding RNAs with presumed post-transcriptional regulatory activity. This term was made obsolete because it implies further processing of an end product rather than its production.
obsolete microRNA biosynthetic process(GO:0010195)biological_processOBSOLETE. The chemical reactions and pathways resulting in the formation of microRNA, a large family of 21-22 nucleotide non-coding RNAs with presumed post-transcriptional regulatory activity. This term was made obsolete because it represents a process that is not known to occur.
chloroplast mRNA processing(GO:0010239)biological_processSteps involved in processing precursor RNAs arising from transcription of operons in the chloroplast genome into mature mRNAs.
response to low fluence blue light stimulus by blue low-fluence system(GO:0010244)biological_processAny process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the detection of a low fluence blue light stimulus by the blue low-fluence system. Blue light is electromagnetic radiation with a wavelength of between 440 and 500nm. The blue low-fluence system responds to blue light at or below 0.1 micromols/m2. In certain species excitation of the blue low fluence system induces the transcription of a number of nuclear and plastid coded genes.
serum response element binding(GO:0010736)molecular_functionInteracting selectively and non-covalently with the serum response element (SRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum.
regulation of chromatin silencing by small RNA(GO:0010964)biological_processAny process that modulates the frequency, rate or extent of chromatin silencing by small RNA. Chromatin silencing by small RNA is the repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region.
gene silencing involved in chronological cell aging(GO:0010978)biological_processAny transcriptional or post-transcriptional process, arising in non-dividing cells as they age, carried out at the cellular level that results in long-term gene inactivation.
Cajal body(GO:0015030)cellular_componentA class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
RISC complex(GO:0016442)cellular_componentA ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.
dosage compensation complex assembly involved in dosage compensation by hyperactivation of X chromosome(GO:0016457)biological_processThe aggregation, arrangement and bonding together of proteins on DNA to form the complex that mediates dosage compensation on the X chromosome of the heterogametic sex, ultimately resulting in a two-fold increase in transcription from this chromosome. An example of this is found in Drosophila melanogaster.
gene silencing(GO:0016458)biological_processAny process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression.
core-binding factor complex(GO:0016513)cellular_componentA heterodimeric transcription factor complex that contains an alpha subunit (Runx1, Runx2 or Runx3 in human) that binds DNA and a non-DNA-binding beta subunit (CBFbeta), and binds to a consensus sequence 5'-YGYGGTY-3' found in several enhancers and promoters; the beta subunit enhances the DNA binding of the alpha subunit.
obsolete insertion or deletion editing(GO:0016550)biological_processOBSOLETE. The insertion into or deletion from an RNA molecule of nucleotide residues not encoded in DNA; takes place during or after transcription. This term was made obsolete because it represents two separate processes (insertion and deletion).
Sin3 complex(GO:0016580)cellular_componentA multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.
NuRD complex(GO:0016581)cellular_componentAn approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.
RSC-type complex(GO:0016586)cellular_componentA SWI/SNF-type complex that contains a bromodomain containing-protein, such as yeast Rsc1 or Rsc4 or mammalian PB1/BAF180. The RSC complex is generally recruited to RNA polymerase III promoters and is specifically recruited to RNA polymerase II promoters by transcriptional activators and repressors; it is also involved in non-homologous end joining
NURF complex(GO:0016589)cellular_componentAn ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters.
ACF complex(GO:0016590)cellular_componentAn ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals, Isw2 in S. cerevisiae), an ACF1 homolog, and generally no other subunits, though Xenopus is an exception with a third non-conserved subunit. ACF plays roles in regulation of RNA polymerase II transcription and in DNA replication and repair.
RNA polymerase II, holoenzyme(GO:0016591)cellular_componentA nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters.
mediator complex(GO:0016592)cellular_componentA protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
Cdc73/Paf1 complex(GO:0016593)cellular_componentA multiprotein complex that associates with RNA polymerase II and general RNA polymerase II transcription factor complexes and may be involved in both transcriptional initiation and elongation. In Saccharomyces the complex contains Paf1p, Cdc73p, Ctr9p, Rtf1p, and Leo1p.
sigma factor antagonist activity(GO:0016989)molecular_functionThe function of binding to a sigma factor and stopping, preventing or reducing the rate of its transcriptional activity.
negative cofactor 2 complex(GO:0017054)cellular_componentA heterodimeric protein complex that can stably associate with TATA-binding protein on promoters, thereby preventing the assembly of transcription factors TFIIA and TFIIB and leading to repression of RNA polymerase II transcription. The two subunits, NC2alpha (Drap1) and NC2beta (Dr1), dimerize through histone fold domains of the H2A/H2B type present in the amino termini.
mineralocorticoid receptor activity(GO:0017082)molecular_functionCombining with a mineralocorticoid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
obsolete sterol regulatory element-binding protein site 2 protease activity(GO:0017092)molecular_functionOBSOLETE. Catalysis of the cleavage, within the membrane-spanning helix, of the amino-terminal half (the intermediate form) of sterol regulatory element binding protein (SREBP). This activity releases the transcription factor domain of SREBP from the membrane, freeing it to enter the nucleus. This term was made obsolete because it represents a gene product.
obsolete sterol regulatory element-binding protein protease activity(GO:0017093)molecular_functionOBSOLETE. Catalysis of the hydrolysis of peptide bonds within a sterol regulatory element binding protein (SREBP). SREBPs are transcription factors that bind sterol regulatory elements (SREs), DNA motifs found in the promoters of target genes. This term was made obsolete because it represents a gene product.
viral gene expression(GO:0019080)biological_processA process by which a viral gene is converted into a mature gene product or products (proteins or RNA). This includes viral transcription, processing to produce a mature RNA product, and viral translation.
cytokine-mediated signaling pathway(GO:0019221)biological_processA series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cyclin-dependent protein kinase activating kinase holoenzyme complex(GO:0019907)cellular_componentA cyclin-dependent kinase activating kinase complex capable of activating cyclin-dependent kinases by threonine phosphorylation, thus regulating cell cycle progression. consists of a kinase, cyclin and optional assembly factors, in human CDK7, CCNH and MNAT1. CAK activity is itself regulated throughout the cell cycle by T-loop phosphorylation of its kinase component (CDK7 in human). Phosphorylation of serine residues during mitosis inactivates the enzyme. Also capable of CAK phosphorylating the carboxyl-terminal domain (CTD) of RNA polymerase II and other transcription activating proteins, as part of the general transcription factor TFIIH.
CD40 signaling pathway(GO:0023035)biological_processA series of molecular signals initiated by the binding of the cell surface receptor CD40 to one of its physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription.
insulin control element activator complex(GO:0030232)cellular_componentTranscription factor complex that binds to the insulin control element (ICE), a DNA sequence element found within the 5'-flanking region of the insulin gene, and activates ICE-mediated transcription.
estrogen receptor activity(GO:0030284)molecular_functionCombining with estrogen and transmitting the signal within the cell to trigger a change in cell activity or function.
thyroid hormone receptor coactivator activity(GO:0030375)molecular_functionThe function of a transcription cofactor that activates transcription in conjunction with a thyroid hormone-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
tRNA methylation(GO:0030488)biological_processThe posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
BMP signaling pathway(GO:0030509)biological_processA series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
intracellular estrogen receptor signaling pathway(GO:0030520)biological_processAny series of molecular signals generated as a consequence of an intracellular estrogen receptor binding to one of its physiological ligands. The pathway begins with receptor-ligand binding, and ends with regulation of a downstream cellular process (e.g. transcription).
rRNA modification guide activity(GO:0030556)molecular_functionSpecifies the site of a posttranscriptional modification in an rRNA molecule by base pairing with a short sequence around the target residue.
tRNA modification guide activity(GO:0030557)molecular_functionSpecifies the site of a posttranscriptional modification in a tRNA molecule by base pairing with a short sequence around the target residue.
snRNA modification guide activity(GO:0030566)molecular_functionSpecifies the site of a posttranscriptional modification in an snRNA molecule by base pairing with a short sequence around the target residue.
Cajal body organization(GO:0030576)biological_processA process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of Cajal bodies, nuclear bodies that appear ultrastructurally as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter and are enriched in ribonucleoproteins, and certain general RNA polymerase II transcription factors.
chromatin silencing at centromere(GO:0030702)biological_processRepression of transcription of centromeric DNA by altering the structure of chromatin.
RENT complex(GO:0030869)cellular_componentA protein complex that mediates transcriptional silencing at the rDNA locus (the name derives from regulator of nucleolar silencing and telophase). In Saccharomyces the complex contains Net1p, Sir2p, Cdc14p, and at least one more subunit.
STAGA complex(GO:0030914)cellular_componentA large multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. The composition is similar to that of the SAGA complex; for example, the human complex contains the transcription-transformation cofactor TRRAP, hGCN5L acetylase, novel human ADA-like and SPT-like cofactors, and a subset of TAFs.
RITS complex(GO:0030958)cellular_componentA protein complex required for heterochromatin assembly; contains an Argonaute homolog, a chromodomain protein, and at least one additional protein; named for RNA-induced initiation of transcriptional gene silencing.
endoplasmic reticulum unfolded protein response(GO:0030968)biological_processThe series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
ISWI-type complex(GO:0031010)cellular_componentAny nuclear protein complex that contains an ATPase subunit of the imitation switch (ISWI) family. ISWI ATPases are involved in assembling chromatin and in sliding and spacing nucleosomes to regulate transcription of nuclear RNA polymerases I, II, and III and also DNA replication, recombination and repair.
macronucleus(GO:0031039)cellular_componentA membrane-bounded organelle of ciliated protozoan cells that contains polyploid copies of a portion of the cell's complete genome. Transcription of genes occurs in macronuclei. Some ciliate species may contain multiple macronuclei per cell.
micronucleus(GO:0031040)cellular_componentA membrane-bounded organelle of ciliated protozoan cells that contains a diploid copy of the cell's complete genome. Sections of contiguous sequence in the macronucleus are often interrupted by internal eliminated sequences (IES), and may be permuted, in micronuclei. Genic transcription is not found in micronuclei. Some ciliate species may contain multiple micronuclei per cell.
rRNA methylation(GO:0031167)biological_processThe posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
POZ domain binding(GO:0031208)molecular_functionInteracting selectively and non-covalently with a POZ (poxvirus and zinc finger) domain of a protein, a protein-protein interaction domain found in many transcription factors.
RSF complex(GO:0031213)cellular_componentAn ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals) and an RSF1 homolog. It mediates nucleosome deposition and generates regularly spaced nucleosome arrays. In mammals, RSF is involved in regulation of transcription from RNA polymerase II promoters).
heterochromatin assembly(GO:0031507)biological_processThe assembly of chromatin into heterochromatin, a compact and highly condensed form that is often, but not always, transcriptionally silent.
Myb complex(GO:0031523)cellular_componentA multisubunit complex consisting of Myb and other proteins that regulates site specific DNA replication, gene amplification and transcriptional repression.
lipopolysaccharide-mediated signaling pathway(GO:0031663)biological_processA series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
cortisol receptor activity(GO:0031963)molecular_functionCombining with cortisol and transmitting the signal within the cell to trigger a change in cell activity or function.
NELF complex(GO:0032021)cellular_componentA complex of five proteins, designated NELF-A, -B, -C, -D, and -E in human, that can physically associate with RNP polymerase II to induce transcriptional pausing.
DSIF complex(GO:0032044)cellular_componentA heterodimeric protein complex formed of Spt4 and Spt5 proteins which is expressed in eukaryotes from yeast to man. DSIF is an inhibitory elongation factor that promotes RNA polymerase II transcriptional pausing, but can also stimulate transcriptional elongation under certain conditions, and may play a role in RNA processing via its physical association with mRNA capping enzymes.
activin responsive factor complex(GO:0032444)cellular_componentA transcriptionally active complex that binds to an activin response element (ARE) in the promoter of target genes, and is composed of two SMAD2 proteins, one SMAD4 protein and a Forkhead activin signal transducer (FAST) transcription factor.
CURI complex(GO:0032545)cellular_componentA protein complex that is involved in the transcription of ribosomal genes. In Saccharomyces this complex consists of Ckb2p, Utp22p, Rrp7p and Ifh1p.
RNA biosynthetic process(GO:0032774)biological_processThe chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
sterol response element binding(GO:0032810)molecular_functionInteracting selectively and non-covalently with the sterol response element (SRE), a nonpalindromic sequence found in the promoters of genes involved in lipid metabolism.
activin receptor signaling pathway(GO:0032924)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
protein-DNA complex(GO:0032993)cellular_componentA macromolecular complex containing both protein and DNA molecules.
regulation of peptidyl-serine phosphorylation of STAT protein(GO:0033139)biological_processAny process that modulates the frequency, rate or extent of the phosphorylation of a serine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
negative regulation of peptidyl-serine phosphorylation of STAT protein(GO:0033140)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of a serine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
positive regulation of peptidyl-serine phosphorylation of STAT protein(GO:0033141)biological_processAny process that activates or increases the frequency, rate or extent of the phosphorylation of a serine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
calcineurin-NFAT signaling cascade(GO:0033173)biological_processAny intracellular signal transduction in which the signal is passed on within the cell by activation of a member of the NFAT protein family as a consequence of NFAT dephosphorylation by Ca(2+)-activated calcineurin. The cascade begins with calcium-dependent activation of the phosphatase calcineurin. Calcineurin dephosphorylates multiple phosphoserine residues on NFAT, resulting in the translocation of NFAT to the nucleus. The cascade ends with regulation of transcription by NFAT. The calcineurin-NFAT cascade lies downstream of many cell surface receptors, including G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs) that signal to mobilize calcium ions (Ca2+).
Lsd1/2 complex(GO:0033193)cellular_componentA nucleosome-binding protein complex that comprises two SWIRM domain histone demethylases and two PHD finger proteins. The complex is involved in transcriptional regulation via heterochromatic silencing and the regulation of chromatin boundary formation, and was first identified in fission yeast.
tumor necrosis factor-mediated signaling pathway(GO:0033209)biological_processA series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
leptin-mediated signaling pathway(GO:0033210)biological_processA series of molecular signals initiated by the binding of leptin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body.
adiponectin-activated signaling pathway(GO:0033211)biological_processA series of molecular signals initiated by the binding of adiponectin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
SAS acetyltransferase complex(GO:0033255)cellular_componentA protein complex that possesses histone acetyltransferase activity and links histone acetylation to the assembly of transcriptionally silent chromatin. In vitro, the complex acetylates lysine 16 of histone H4 and lysine 14 of histone H3, although the latter may not be relevant in vivo. The complex contains a catalytic subunit and at least two other subunits; in Saccharomyces, the catalytic subunit is Sas2p and additional subunits are Sas4p and Sas5p.
Bcl3/NF-kappaB2 complex(GO:0033257)cellular_componentA protein complex containing one Bcl protein and one or more copies of NF-kappaB2; formation of complexes of different stoichiometry depends on the Bcl3:NF-kappaB2 ratio, and allow Bcl3 to exert different regulatory effects on NF-kappaB2-dependent transcription.
Elongator holoenzyme complex(GO:0033588)cellular_componentA heterohexameric protein complex that is involved in modification of wobble nucleosides in tRNA. The complex can associate physically with hyperphosphorylated RNA polymerase II; it contains two discrete heterotrimeric subcomplexes.
estrogen response element binding(GO:0034056)molecular_functionInteracting selectively and non-covalently with the estrogen response element (ERE), a conserved sequence found in the promoters of genes whose expression is regulated in response to estrogen.
Tor2-Mei2-Ste11 complex(GO:0034064)cellular_componentA protein complex that contains the transcription factor Ste11 and the RNA binding protein Mei2; involved in regulation of conjugation in fission yeast.
enhanceosome(GO:0034206)cellular_componentA protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation.
mitochondrial unfolded protein response(GO:0034514)biological_processThe series of molecular signals generated as a consequence of the presence of unfolded proteins in the mitochondrial matrix; results in transcriptional upregulation of nuclear genes encoding mitochondrial stress proteins.
TFIIIC-TOP1-SUB1 complex(GO:0034740)cellular_componentA protein complex that contains TFIIIC, topoisomerase 1, and Sub1/PC4. Characterized in human, the complex is involved in regulating transcription from RNA polymerase III (Pol III) promoters. Topoisomerase 1 and Sub1 enhance the accuracy of transcription termination, and promote reinitiation by Pol III.
Set3 complex(GO:0034967)cellular_componentA histone deacetylase complex that is involved in transcriptional regulation. In S. cerevisiae, this complex consists of Set3p, Snt1p, Hos4p, Sif2p, Cpr1p, Hos2p, and Hst1p.
PDX1-PBX1b-MRG1 complex(GO:0034978)cellular_componentA protein complex that contains the homeodomain proteins PDX1, PBX1b and MRG1 (MEIS2) and is involved in the transcriptional regulation of pancreatic acinar cell-specific genes.
FHL2-CREB complex(GO:0034980)cellular_componentA protein complex that contains CREB and FHL2, and is involved in transcriptional regulation.
FHL3-CREB complex(GO:0034981)cellular_componentA protein complex that contains CREB and FHL3, and is involved in transcriptional regulation.
polytene chromosome puffing(GO:0035079)biological_processThe decondensing (loosening) and swelling of the chromosomal sites of target genes on polytene chromosomes following response to a stimulus, to facilitate sudden bursts of transcriptional activity in response to transient environmental signals.
sperm chromatin condensation(GO:0035092)biological_processThe progressive compaction of the spermatid chromatin so that it reaches a level of condensation that is not compatible with nuclear activities such as transcription or DNA replication.
PRC1 complex(GO:0035102)cellular_componentA multiprotein complex that mediates monoubiquitination of lysine residues of histone H2A (lysine-118 in Drosophila or lysine-119 in mammals). The complex is required for stable long-term maintenance of transcriptionally repressed states and is involved in chromatin remodeling.
sterol regulatory element binding protein cleavage(GO:0035103)biological_processThe proteolytic release of a transcriptionally active sterol regulatory element binding protein (SREBP) from intracellular membranes, freeing it to move to the nucleus to upregulate transcription of target genes, in response to altered levels of one or more lipids.
obsolete sterol regulatory element binding protein import into nucleus(GO:0035105)biological_processOBSOLETE. The transfer of a sterol regulatory element binding protein (SREBP) into the nucleus, across the nuclear membrane, in response to altered levels of one or more lipids. SREBPs are transcription factors that bind sterol regulatory elements (SREs), DNA motifs found in the promoters of target genes. The reason for obsoletion is that all proteins are imported into the nucleus via the same mechanism, so the import of individual proteins should be captured with extensions or by GO-CAM models.
Rb-E2F complex(GO:0035189)cellular_componentA multiprotein complex containing a heterodimeric E2F transcription factor and a Retinoblastoma (Rb) family member. This complex is capable of repressing transcription of E2F-regulated genes in order to regulate cell cycle progression.
gene silencing by miRNA(GO:0035195)biological_processDownregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endolytic cleavage of mRNA cleavage or translational repression, usually accompanied by poly-A tail shortening and subsequent degradation of the mRNA.
ionotropic glutamate receptor signaling pathway(GO:0035235)biological_processA series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
Hedgehog signaling complex(GO:0035301)cellular_componentA multiprotein complex that binds microtubules in a Hedgehog-dependent manner, and is required for signal transduction by members of the Hedgehog family of proteins. The core components of the complex are the serine/threonine protein kinase Fused, the kinesin motor protein Costal2 (Cos2), and a zinc finger transcription factor (Gli family members in humans, and Cubitus interruptus (Ci) in Drosophila).
enhancer binding(GO:0035326)molecular_functionInteracting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
hippo signaling(GO:0035329)biological_processThe series of molecular signals mediated by the serine/threonine kinase Hippo or one of its orthologs. In Drosophila, Hippo in complex with the scaffold protein Salvador (Sav), phosphorylates and activates Warts (Wts), which in turn phosphorylates and inactivates the Yorkie (Yki) transcriptional activator. The core fly components hippo, sav, wts and mats are conserved in mammals as STK4/3 (MST1/2), SAV1/WW45, LATS1/2 and MOB1.
peroxisome proliferator activated receptor signaling pathway(GO:0035357)biological_processThe series of molecular signals initiated by binding of a ligand to any of the peroxisome proliferator activated receptors (alpha, beta or gamma) in the nuclear membrane, and ending with the initiation or termination of the transcription of target genes.
histone locus body(GO:0035363)cellular_componentA nuclear body associated with the histone gene locus that is thought to contain all of the factors necessary for histone mRNA transcription and pre-mRNA processing. In Drosophila, U7 snRNP is located in the histone locus body rather than the distinct Cajal body.
Roundabout signaling pathway(GO:0035385)biological_processA series of molecular signals initiated by the binding of a SLIT protein to a Roundabout (ROBO) family receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
establishment of chromatin silencing at silent mating-type cassette(GO:0035389)biological_processThe initial formation of a transcriptionally silent chromatin structure such as heterochromatin at silent mating-type loci.
establishment of chromatin silencing at telomere(GO:0035390)biological_processThe initial formation of a transcriptionally silent chromatin structure such as heterochromatin at the telomere.
maintenance of chromatin silencing at silent mating-type cassette(GO:0035391)biological_processThe maintenance of chromatin in a transcriptionally silent state such as heterochromatin at silent mating-type loci.
maintenance of chromatin silencing at telomere(GO:0035392)biological_processThe maintenance of chromatin in a transcriptionally silent state such as heterochromatin at the telomere.
cAMP response element binding(GO:0035497)molecular_functionInteracting selectively and non-covalently with the cyclic AMP response element (CRE), a short palindrome-containing sequence found in the promoters of genes whose expression is regulated in response to cyclic AMP.
MH1 domain binding(GO:0035501)molecular_functionInteracting selectively and non-covalently with the MH1 (MAD homology 1) domain of a protein. The MH1 domain is found at the amino terminus of MAD related proteins such as Smads and can mediate DNA binding in some proteins. Smads also use the MH1 domain to interact with some transcription factors.
carbohydrate response element binding(GO:0035538)molecular_functionInteracting selectively and non-covalently with the carbohydrate response element (ChoRE) found in the promoters of genes whose expression is regulated in response to carbohydrates, such as the triglyceride synthesis genes.
Nrd1 complex(GO:0035649)cellular_componentA complex that functions in transcription termination of RNA polymerase II transcribed non-coding RNAs. This complex interacts with the carboxy-terminal domain (CTD) of PolII and the terminator sequences in the nascent RNA transcript. In yeast this complex consists of Nrd1p, Nab3p, and Sen1p.
interleukin-18-mediated signaling pathway(GO:0035655)biological_processA series of molecular signals initiated by the binding of interleukin-18 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
chemokine (C-C motif) ligand 5 signaling pathway(GO:0035689)biological_processA series of molecular signals initiated by the binding of the chemokine CCL5 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
macrophage migration inhibitory factor signaling pathway(GO:0035691)biological_processA series of molecular signals initiated by the binding of macrophage migration inhibitory factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-12-mediated signaling pathway(GO:0035722)biological_processA series of molecular signals initiated by the binding of interleukin-12 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-15-mediated signaling pathway(GO:0035723)biological_processA series of molecular signals initiated by the binding of interleukin-15 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-4-mediated signaling pathway(GO:0035771)biological_processA series of molecular signals initiated by the binding of interleukin-4 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-13-mediated signaling pathway(GO:0035772)biological_processA series of molecular signals initiated by the binding of interleukin-13 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
platelet-derived growth factor receptor-alpha signaling pathway(GO:0035790)biological_processA series of molecular signals initiated by the binding of a ligand to an alpha-type platelet-derived growth factor receptor (PDGFalpha) on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
platelet-derived growth factor receptor-beta signaling pathway(GO:0035791)biological_processA series of molecular signals initiated by the binding of a ligand to a beta-type platelet-derived growth factor receptor (PDGFbeta) on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
Krueppel-associated box domain binding(GO:0035851)molecular_functionInteracting selectively and non-covalently with a Krueppel-associated box (KRAB) domain of a protein. The approximately 75 amino acid KRAB domain is enriched in charged amino acids, and is found in the N-terminal regions of many zinc finger-containing transcription factors.
senescence-associated heterochromatin focus(GO:0035985)cellular_componentA transcriptionally-silent heterochromatin structure present in senescent cells. Contains the condensed chromatin of one chromosome and is enriched for histone modifications. Thought to repress expression of proliferation-promoting genes.
senescence-associated heterochromatin focus assembly(GO:0035986)biological_processThe assembly of chromatin into senescence-associated heterochromatin foci (SAHF), transcriptionally-silent heterochromatin structures present in senescent cells, containing the condensed chromatin of one chromosome, and enriched for histone modifications. Formation of these chromatin structures is thought to repress expression of proliferation-promoting genes.
mediator complex binding(GO:0036033)molecular_functionInteracting selectively and non-covalently with a mediator complex. The mediator complex is a protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
mediator complex assembly(GO:0036034)biological_processThe aggregation, arrangement and bonding together of a set of components to form a mediator complex. The mediator complex is a protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
interstrand cross-link repair(GO:0036297)biological_processRemoval of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA. DNA interstrand crosslinks occur when both strands of duplex DNA are covalently tethered together (e.g. by an exogenous or endogenous agent), thus preventing the strand unwinding necessary for essential DNA functions such as transcription and replication.
vascular endothelial growth factor receptor-1 signaling pathway(GO:0036323)biological_processAny series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor-1 (VEGFR-1) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
vascular endothelial growth factor receptor-2 signaling pathway(GO:0036324)biological_processAny series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor-2 (VEGFR-2) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
vascular endothelial growth factor receptor-3 signaling pathway(GO:0036325)biological_processAny series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor-3 (VEGFR-3) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
Fas signaling pathway(GO:0036337)biological_processA series of molecular signals initiated by the binding of a ligand to the receptor Fas on the surface of the cell, and ending with regulation of a downstream cellular process, e.g. transcription. Fas is a death domain-containing member of the tumor necrosis factor receptor (TNFR) superfamily.
RNA N6-methyladenosine methyltransferase complex(GO:0036396)cellular_componentA RNA methyltransferase complex that catalyzes the post-transcriptional methylation of adenosine to form N6-methyladenosine (m6A). In budding yeast, the MIS complex consists of Mum2p, Ime4p and Slz1p. In vertebrates, the complex consists of METTL3, METTL14 and associated components WTAP, ZC3H13, VIRMA, CBLL1/HAKAI and in some cases of RBM15 (RBM15 or RBM15B).
H-NS-Cnu complex(GO:0036411)cellular_componentA trimeric protein complex containing a H-NS homodimer and a Cnu monomer. In bacteria, this complex negatively regulates transcription of a range of genes.
CHOP-C/EBP complex(GO:0036488)cellular_componentA heterodimeric protein complex that is composed of the transcription factor CHOP (GADD153) and a member of the C/EBP family of transcription factors.
PERK-mediated unfolded protein response(GO:0036499)biological_processA series of molecular signals mediated by the endoplasmic reticulum membrane stress sensor PERK (PKR-like ER kinase). Begins with activation of PERK in response to endoplasmic reticulum (ER) stress and ends with regulation of a downstream cellular process, e.g. transcription. The main substrate of PERK is the translation initiation factor eIF2alpha. Serine-phosphorylation of eIF2alpha by PERK inactivates eIF2alpha and inhibits general protein translation. In addition, eIF2alpha phosphorylation preferentially increases the translation of selective mRNAs such as ATF4 (activating transcription factor 4), which up regulates a subset of UPR genes required to restore folding capacity.
netrin-activated signaling pathway(GO:0038007)biological_processA series of molecular events initiated by the binding of a netrin protein to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Netrins can act as chemoattractant signals for some cells and chemorepellent signals for others. Netrins also have roles outside of cell and axon guidance.
reelin-mediated signaling pathway(GO:0038026)biological_processA series of molecular signals initiated by the binding of reelin (a secreted glycoprotein) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
apolipoprotein A-I-mediated signaling pathway(GO:0038027)biological_processA series of molecular signals initiated by the binding of apolipoprotein A-I to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-5-mediated signaling pathway(GO:0038043)biological_processA series of molecular signals initiated by the binding of interleukin-5 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
collagen-activated tyrosine kinase receptor signaling pathway(GO:0038063)biological_processA series of molecular signals initiated by the binding of collagen to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
collagen-activated signaling pathway(GO:0038065)biological_processA series of molecular signals initiated by collagen binding to a cell surface receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
vascular endothelial growth factor signaling pathway(GO:0038084)biological_processA series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
VEGF-activated platelet-derived growth factor receptor signaling pathway(GO:0038086)biological_processA series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a platelet-derived growth factor receptor (PDGFR) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
VEGF-activated platelet-derived growth factor receptor-alpha signaling pathway(GO:0038087)biological_processA series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to an alpha-type platelet-derived growth factor receptor (PDGFR) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
VEGF-activated platelet-derived growth factor receptor-beta signaling pathway(GO:0038088)biological_processA series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a beta-type platelet-derived growth factor receptor (PDGFR) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
nodal signaling pathway(GO:0038092)biological_processA series of molecular signals initiated by the binding of a nodal protein to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
Fc receptor signaling pathway(GO:0038093)biological_processA series of molecular signals initiated by the binding of the Fc portion of an immunoglobulin to an Fc receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
Fc-gamma receptor signaling pathway(GO:0038094)biological_processA series of molecular signals initiated by the binding of the Fc portion of immunoglobulin G (IgG) to an Fc-gamma receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
Fc-epsilon receptor signaling pathway(GO:0038095)biological_processA series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
Kit signaling pathway(GO:0038109)biological_processA series of molecular signals that starts with the binding of stem cell factor to the tyrosine kinase receptor KIT on the surface of a cell, and ends with regulation of a downstream cellular process, e.g. transcription. Stem cell factor (KIT ligand) binding to the receptor Kit mediates receptor dimerization, activation of its intrinsic tyrosine kinase activity and autophosphorylation. The activated receptor then phosphorylates various substrates, thereby activating distinct signaling cascades within the cell that trigger a change in state or activity of the cell.
interleukin-2-mediated signaling pathway(GO:0038110)biological_processA series of molecular signals initiated by the binding of interleukin-2 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-7-mediated signaling pathway(GO:0038111)biological_processA series of molecular signals initiated by the binding of interleukin-7 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-8-mediated signaling pathway(GO:0038112)biological_processA series of molecular signals initiated by the binding of interleukin-8 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-9-mediated signaling pathway(GO:0038113)biological_processA series of molecular signals initiated by the binding of interleukin-9 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-21-mediated signaling pathway(GO:0038114)biological_processA series of molecular signals initiated by the binding of interleukin-21 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
chemokine (C-C motif) ligand 19 signaling pathway(GO:0038115)biological_processA series of molecular signals initiated by the binding of the C-C chemokine CCL19 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
chemokine (C-C motif) ligand 21 signaling pathway(GO:0038116)biological_processA series of molecular signals initiated by the binding of the C-C chemokine CCL21 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
C-C chemokine receptor CCR7 signaling pathway(GO:0038118)biological_processA series of molecular signals initiated by a the C-C chemokine type 7 receptor on the surface of a cell binding to one of it's physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription.
CCL19-activated CCR7 signaling pathway(GO:0038119)biological_processA series of molecular signals initiated by the binding of the C-C chemokine CCL19 to a C-C chemokine type 7 receptor (CCR7) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
CCL21-activated CCR7 signaling pathway(GO:0038120)biological_processA series of molecular signals initiated by the binding of the C-C chemokine CCL21 to a C-C chemokine type 7 receptor (CCR7) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
toll-like receptor TLR1:TLR2 signaling pathway(GO:0038123)biological_processA series of molecular signals initiated by the binding of a heterodimeric TLR1:TLR2 complex to one of it's physiological ligands, followed by transmission of the signal by the activated receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
toll-like receptor TLR6:TLR2 signaling pathway(GO:0038124)biological_processA series of molecular signals initiated by the binding of a heterodimeric TLR6:TLR2 complex to one of it's physiological ligands, followed by transmission of the signal by the activated receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
ERBB signaling pathway(GO:0038127)biological_processA series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptor tyrosine kinases on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
ERBB2 signaling pathway(GO:0038128)biological_processA series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
ERBB3 signaling pathway(GO:0038129)biological_processA series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB3 on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB3 receptors have impaired kinase activity and rely on the kinase activity of the heterodimer partner for activation and signal transmission.
ERBB4 signaling pathway(GO:0038130)biological_processA series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB4 on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
ERBB3-ERBB4 signaling pathway(GO:0038136)biological_processA series of molecular signals transmitted by a heterodimeric complex of the tyrosine kinase receptors ERBB3 and ERBB4. The pathway begins with binding of a ligand to either cell surface receptor, or the dimeric receptor complex, and ends with regulation of a downstream cellular process, e.g. transcription.
ERBB4-EGFR signaling pathway(GO:0038137)biological_processA series of molecular signals transmitted by a heterodimeric complex of the tyrosine kinase receptors EGFR (epidermal growth factor receptor/ERBB1) and ERBB4. The pathway begins with binding of a ligand to either cell surface receptor, or the dimeric receptor complex, and ends with regulation of a downstream cellular process, e.g. transcription.
ERBB4-ERBB4 signaling pathway(GO:0038138)biological_processA series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB4, followed by ligand-induced homodimerization of ERBB4 and transmission of the signal into the cell by the homodimeric ERBB4 complex. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
macrophage colony-stimulating factor signaling pathway(GO:0038145)biological_processA series of molecular signals initiated by the binding of the cytokine macrophage colony-stimulating factor (M-CSF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
chemokine (C-X-C motif) ligand 12 signaling pathway(GO:0038146)biological_processA series of molecular signals initiated by the binding of the chemokine CXCL12 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
chemokine (C-C motif) ligand 2 signaling pathway(GO:0038148)biological_processA series of molecular signals initiated by the binding of the C-C chemokine CCL2 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
C-C chemokine receptor CCR2 signaling pathway(GO:0038150)biological_processA series of molecular signals initiated by a the C-C chemokine type 2 receptor (CCR2) on the surface of a cell binding to one of it's physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription.
CCL2-activated CCR2 signaling pathway(GO:0038151)biological_processA series of molecular signals initiated by the binding of the C-C chemokine CCL2 to a C-C chemokine type 2 receptor (CCR2) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
C-C chemokine receptor CCR4 signaling pathway(GO:0038152)biological_processA series of molecular signals initiated by a the C-C chemokine type 2 receptor (CCR4) on the surface of a cell binding to one of it's physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription.
CCL2-activated CCR4 signaling pathway(GO:0038153)biological_processA series of molecular signals initiated by the binding of the C-C chemokine CCL2 to a C-C chemokine type 4 receptor (CCR4) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-11-mediated signaling pathway(GO:0038154)biological_processA series of molecular signals initiated by the binding of interleukin-11 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-23-mediated signaling pathway(GO:0038155)biological_processA series of molecular signals initiated by the binding of interleukin-23 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-3-mediated signaling pathway(GO:0038156)biological_processA series of molecular signals initiated by the binding of interleukin-3 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
granulocyte-macrophage colony-stimulating factor signaling pathway(GO:0038157)biological_processA series of molecular signals initiated by the binding of the cytokine granulocyte macrophage colony-stimulating factor (GM-CSF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. GM-CSF binds to a heterodimer receptor (CSF2R) consisting of an alpha ligand-binding subunit, and a common beta subunit that is shared with other cytokine receptors.
granulocyte colony-stimulating factor signaling pathway(GO:0038158)biological_processA series of molecular signals initiated by the binding of the cytokine granulocyte colony-stimulating factor (G-CSF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. G-CSF binds to the receptor (CSF3R).
C-X-C chemokine receptor CXCR4 signaling pathway(GO:0038159)biological_processA series of molecular signals initiated by a the C-X-C chemokine type 4 receptor on the surface of a cell binding to one of it's physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription.
CXCL12-activated CXCR4 signaling pathway(GO:0038160)biological_processA series of molecular signals initiated by the binding of the C-X-C chemokine CXCL12 to a C-X-C chemokine type 4 receptor (CXCR4) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
prolactin signaling pathway(GO:0038161)biological_processA series of molecular signals initiated by the binding of the peptide hormone prolactin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
erythropoietin-mediated signaling pathway(GO:0038162)biological_processA series of molecular signals initiated by the binding of erythropoietin (EPO) to the erythropoietin receptor (EPO-R) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
thrombopoietin-mediated signaling pathway(GO:0038163)biological_processA series of molecular signals initiated by the binding of a thrombopoietin to the thrombopoietin receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
oncostatin-M-mediated signaling pathway(GO:0038165)biological_processA series of molecular signals initiated by the binding of oncostatin-M (OSM) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. OSM can signal via at least two different receptors (a specific receptor and a LIF receptor) to activate different downstream signal transduction pathways.
angiotensin-activated signaling pathway(GO:0038166)biological_processThe series of molecular signals generated as a consequence of angiotensin II binding to an angiotensin receptor on the surface of the cell, and proceeding with the activated receptor transmitting the signal to a heterotrimeric G-protein complex to initiate a change in cell activity. Ends with regulation of a downstream cellular process, e.g. transcription.
epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade(GO:0038168)biological_processThe series of molecular signals generated as a consequence of an epidermal growth factor receptor binding to one of its physiological ligands, where the signal is passed on within the cell via I-kappaB-kinase (IKK)-dependent activation of the transcription factor NF-kappaB.
somatostatin receptor signaling pathway(GO:0038169)biological_processThe series of molecular signals generated as a consequence of a somatostatin receptor (SSTR) binding to one of its physiological ligands and transmitting the signal to a heterotrimeric G-protein complex. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
somatostatin signaling pathway(GO:0038170)biological_processThe series of molecular signals generated as a consequence of the peptide somatostatin (SST) binding to a somatostatin receptor (SSTR). The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription.
cannabinoid signaling pathway(GO:0038171)biological_processThe series of molecular signals generated as a consequence of a cannabinoid binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription. Cannabinoids are a class of diverse chemical compounds that include the endocannabinoids and the phytocannabinoids.
interleukin-33-mediated signaling pathway(GO:0038172)biological_processA series of molecular signals initiated by the binding of interleukin-33 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-17A-mediated signaling pathway(GO:0038173)biological_processA series of molecular signals initiated by the binding of interleukin-17A to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
neurotrophin signaling pathway(GO:0038179)biological_processA series of molecular signals initiated by the binding of a neurotrophin to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Neurotrophins are a family of secreted growth factors that induce the survival, development, and function of neurons.
nerve growth factor signaling pathway(GO:0038180)biological_processA series of molecular signals initiated by the binding of nerve growth factor (NGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
bile acid signaling pathway(GO:0038183)biological_processA series of molecular signals initiated by the binding of a bile acid to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
cell surface bile acid receptor signaling pathway(GO:0038184)biological_processA series of molecular signals initiated by binding of a bile acid to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
intracellular bile acid receptor signaling pathway(GO:0038185)biological_processA series of molecular signals initiated by a bile acid binding to an receptor located within a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cholecystokinin signaling pathway(GO:0038188)biological_processThe series of molecular signals generated as a consequence of cholecystokinin binding to a receptor on the surface of the cell, and proceeding with the activated receptor transmitting the signal to a heterotrimeric G-protein complex to initiate a change in cell activity. Ends with regulation of a downstream cellular process, e.g. transcription.
neuropilin signaling pathway(GO:0038189)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to a neuropilin protein on the surface of a target cell, followed by transmission of the signal, and ending with regulation of a downstream cellular process, e.g. transcription.
VEGF-activated neuropilin signaling pathway(GO:0038190)biological_processA series of molecular signals initiated by the binding of vascular endothelial growth factor (VEGF) to a neuropilin protein on the surface of a target cell, followed by transmission of the signal, and ending with regulation of a downstream cellular process, e.g. transcription.
gastric inhibitory peptide signaling pathway(GO:0038192)biological_processThe series of molecular signals generated as a consequence of a gastric inhibitory peptide (GIP) binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription.
thromboxane A2 signaling pathway(GO:0038193)biological_processThe series of molecular signals generated as a consequence of thromboxane A2 binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription.
thyroid-stimulating hormone signaling pathway(GO:0038194)biological_processThe series of molecular signals generated as a consequence of thyroid-stimulating hormone (thyrotropin) binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription.
urokinase plasminogen activator signaling pathway(GO:0038195)biological_processA series of molecular signals initiated by the binding of urokinase plasminogen activator to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
type III interferon signaling pathway(GO:0038196)biological_processA series of molecular signals initiated by the binding of a type III interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon lambda is the only member of the type III interferon found so far.
obsolete suppression by virus of host RIG-I activity by viral RNA 5' processing(GO:0039543)biological_processOBSOLETE. The post-transcriptional removal by a virus of the 5' triphosphate group of their viral RNA, thereby preventing host RIG-I from recognizing viral RNA in the host cell. The intracellular pattern recognition receptor RIG-I (also known as DDX58) recognizes viral RNAs containing 5' triphosphates; removal by the virus of the 5'-terminal triphosphate group from their genome protects the viral RNA from RIG-recognition. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
suppression by virus of host IRF3 activity(GO:0039548)biological_processAny process in which a virus stops, prevents, or reduces the activity of host IRF3 (interferon regulatory factor-3), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF3, which allows IRF3 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes.
obsolete suppression by virus of host IRF3 activity by inhibition of IRF3 phosphorylation(GO:0039549)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces the rate or extent of the phosphorylation of IRF3 (interferon regulatory factor-3), thereby inhibiting IRF3 activation. In response to signaling from RIG-1/MDA-5 receptors, IRF3 is phosphorylated on multiple serine and threonine residues; phosphorylation results in the cytoplasm-to-nucleus translocation of IRF3, DNA binding, and increased transcriptional activation of interferon-encoding genes. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
obsolete suppression by virus of host IRF3 activity by inhibition of DNA binding(GO:0039550)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces IRF3-dependent gene transcription, by preventing or reducing IRF3 binding to promoter sites. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
suppression by virus of host IRF7 activity(GO:0039557)biological_processAny process in which a virus stops, prevents, or reduces the activity of host IRF7 (interferon regulatory factor-7), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF7, which allows IRF7 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes.
obsolete suppression by virus of host IRF7 activity by positive regulation of IRF7 sumoylation(GO:0039558)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces IRF7-dependent gene transcription, by promoting the sumoylation of IRF7, thereby disabling its activity. The reason for obsoleting is that the term is too specific. The exact molecular roles of the individual proteins should be captured separately.
suppression by virus of host IRF9 activity(GO:0039560)biological_processAny process in which a virus stops, prevents, or reduces the activity of host IRF9 (interferon regulatory factor-9), a transcription factor involved in the innate immune response. Viral infection triggers binding of IRF9 to phosphorylated STAT1 and STAT2, forming the ISGF3 complex. The ISGF3 complex migrates to the nucleus and activates transcription of IFN-responsive genes.
suppression by virus of host STAT1 activity(GO:0039563)biological_processAny process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT1 (signal transducer and activator of transcription-1) activity. STATs are SH2 domain-containing proteins which lie downstream of many signaling receptors. Upon phosphorylation by JAKs, STAT proteins hetero- or homo-dimerize and translocate to the nucleus to activate transcription of target genes.
suppression by virus of host STAT2 activity(GO:0039564)biological_processAny process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT2 (signal transducer and activator of transcription-2) activity. STATs are SH2 domain-containing proteins which lie downstream of many signaling receptors. Upon phosphorylation by JAKs, STAT proteins hetero- or homo-dimerize and translocate to the nucleus to activate transcription of target genes.
obsolete suppression by virus of host STAT1 activity by positive regulation of STAT1 catabolic process(GO:0039565)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces the activity of host STAT1 (signal transducer and activator of transcription-1) by promoting the ubiquitin-dependent degradation of STAT1, mediated by the proteasome. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
obsolete suppression by virus of host STAT1 activity by tyrosine dephosphorylation of STAT1(GO:0039566)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT1 (signal transducer and activator of transcription-1) activity by the removal of phosphoric residues from STAT1-O-phospho-tyrosine to form STAT1-tyrosine. For example, the viral phosphatase VH1 dephosphorylates STAT1 to reverse STAT1 activation. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
obsolete suppression by virus of host STAT1 activity by negative regulation of STAT protein import into nucleus(GO:0039567)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT1 (signal transducer and activator of transcription-1) activity by retaining STAT1 in the cytoplasm, so STAT1 is unable to translocate to the nucleus to activate transcription of its target genes. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
obsolete suppression by virus of host STAT1 activity by inhibition of DNA binding(GO:0039568)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces STAT1-dependent gene transcription, by preventing STAT1 from binding to promoter sites in the nucleus. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
obsolete suppression by virus of host STAT2 activity by positive regulation of STAT2 catabolic process(GO:0039569)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces the activity of host STAT2 (signal transducer and activator of transcription-2) by promoting the ubiquitin-dependent degradation of STAT2, mediated by the proteasome. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
obsolete suppression by virus of host STAT2 activity by negative regulation of STAT protein import into nucleus(GO:0039570)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT2 (signal transducer and activator of transcription-2) activity by retaining STAT2 in the cytoplasm, so STAT2 is unable to translocate to the nucleus to activate transcription of its target genes. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
obsolete suppression by virus of host STAT1 activity by negative regulation of STAT1 tyrosine phosphorylation(GO:0039571)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT1 (signal transducer and activator of transcription-1) activity by stopping, preventing, or reducing the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a STAT1 protein. For example, the measles virus V protein inhibits tyrosine phosphorylation of STAT1, thereby preventing STAT1 activation. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
obsolete suppression by virus of host STAT2 activity by negative regulation of STAT2 tyrosine phosphorylation(GO:0039572)biological_processOBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT2 (signal transducer and activator of transcription-2) activity by stopping, preventing, or reducing the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a STAT2 protein. For example, the measles virus V protein inhibits tyrosine phosphorylation of STAT2, thereby preventing STAT2 activation. The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
PKR signal transduction(GO:0039585)biological_processA series of reactions in which a signal is passed on to downstream proteins within the cell via PKR, an intracellular protein kinase that is activated by stress signals or upon binding to double-stranded RNA (dsRNA), followed by autophosphorylation. PKR plays a role in the antiviral response, phosphorylating proteins such as the translation initiation factor eIF2 to inhibit protein synthesis during viral infection. Begins with activation of PKR activity, and ends with regulation of a downstream cellular process, e.g. regulation of transcription or inhibition of translation.
polyadenylation of viral mRNA by polymerase stuttering(GO:0039698)biological_processPolyadenylation of viral mRNA through a polymerase stuttering mechanism. The stop signal present at the end of each gene comprises a stretch of uridine on which the viral polymerase acquires a stuttering behavior: after each adenine inserted, the polymerase moves back one nucleotide along with the mRNA. It resumes transcription adding a new adenine, then again moves back, thereby producing a polyA tail.
RNA-mediated DNA recombination(GO:0042152)biological_processThe reverse transcription of an RNA molecule followed by recombination between the resultant cDNA and its homologous chromosomal allele.
serine phosphorylation of STAT protein(GO:0042501)biological_processThe process of introducing a phosphate group to a serine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
regulation of tyrosine phosphorylation of STAT protein(GO:0042509)biological_processAny process that modulates the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
positive regulation of tyrosine phosphorylation of STAT protein(GO:0042531)biological_processAny process that activates or increases the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
negative regulation of tyrosine phosphorylation of STAT protein(GO:0042532)biological_processAny process that stops, prevents, or reduces the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
biofilm formation(GO:0042710)biological_processA process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
dosage compensation complex assembly involved in dosage compensation by hypoactivation of X chromosome(GO:0042715)biological_processThe aggregation, arrangement and bonding together of proteins on DNA to form the complex that mediates dosage compensation on both X chromosomes in the monogametic sex, ultimately resulting in a two-fold reduction in transcription from these chromosomes. An example of this process is found in Caenorhabditis elegans.
vitamin D receptor binding(GO:0042809)molecular_functionInteracting selectively and non-covalently with the vitamin D receptor, a nuclear receptor that mediates the action of vitamin D by binding DNA and controlling the transcription of hormone-sensitive genes.
retinoic acid receptor binding(GO:0042974)molecular_functionInteracting selectively and non-covalently with the retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily.
ATP-dependent chromatin remodeling(GO:0043044)biological_processDynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
rDNA spacer replication fork barrier binding(GO:0043110)molecular_functionInteracting selectively and non-covalently with replication fork barriers found in rDNA spacers, sites that inhibit replication forks in the direction opposite to rDNA transcription.
HLH domain binding(GO:0043398)molecular_functionInteracting selectively and non-covalently with Helix Loop Helix, a domain of 40-50 residues that occurs in specific DNA-binding proteins that act as transcription factors. The domain is formed of two amphipathic helices joined by a variable length linker region that can form a loop and it mediates protein dimerization.
MRF binding(GO:0043426)molecular_functionInteracting selectively and non-covalently with Myogenic Regulatory Factor (MRF), a member of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors.
Ku70:Ku80 complex(GO:0043564)cellular_componentHeterodimeric protein complex composed of a 70 kDa and a 80 kDa subunit, binds DNA through a channel formed by the heterodimer. Functions in DNA double stranded break repair, chromosome maintenance, transcription regulation, V(D)J recombination, and activation of DNA-PK.
maintenance of CRISPR repeat elements(GO:0043571)biological_processAny process involved in sustaining CRISPR repeat clusters, including capture of new spacer elements, expansion or contraction of clusters, propagation of the leader sequence and repeat clusters within a genome, transfer of repeat clusters and CRISPR-associated (cas) genes to new genomes, transcription of the CRISPR repeat arrays into RNA and processing, and interaction of CRISPR/cas loci with the host genome. CRISPR (clustered regularly interspaced short palindromic repeat) elements are a family of sequence elements containing multiple direct repeats of 24-48 bp with weak dyad symmetry which are separated by regularly sized nonrepetitive spacer sequences.
ncRNA polyadenylation(GO:0043629)biological_processThe enzymatic addition of a sequence of adenylyl residues at the 3' end of a non-coding RNA (ncRNA) molecule. In eukaryotes, substrates include nuclear non-coding RNAs such as precursors and a variety of incorrectly processed forms of snRNAs, snoRNAs, rRNAs, and tRNAs, as well as discarded RNA fragments which have been removed from ncRNA primary transcripts. Polyadenylation of precursors is often linked to termination of transcription, but polyadenylation of RNAs targeted for degradation may also occur post-transcriptionally. This polyadenylation is important both for 3'-end processing to produce mature ncRNA species and also for targeting incorrectly processed or discarded RNA molecules for degradation.
single-species biofilm formation(GO:0044010)biological_processA process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
single-species biofilm formation on inanimate substrate(GO:0044011)biological_processA process in which microorganisms of the same species attach to and grow on an inanimate surface such as a rock or pipe, and produce extracellular polymers that facilitate attachment and matrix formation, resulting in an alteration in the phenotype of the organisms with respect to growth rate and gene transcription.
hypermethylation of CpG island(GO:0044027)biological_processAn increase in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes.
hypomethylation of CpG island(GO:0044029)biological_processAn decrease in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes.
Rel homology domain binding(GO:0044197)molecular_functionInteracting selectively and non-covalently with a Rel Homology Domain (RHD) of a protein. The RHD is found in a family of eukaryotic transcription factors, which includes NF-kappaB, Dorsal, Relish and NFAT.
retinoic acid-responsive element binding(GO:0044323)molecular_functionInteracting selectively and non-covalently with a retinoic acid-responsive element, a variable direct repeat of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.
canonical Wnt signaling pathway involved in positive regulation of endothelial cell migration(GO:0044328)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in the positive regulation of endothelial cell migration.
canonical Wnt signaling pathway involved in positive regulation of cell-cell adhesion(GO:0044329)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in the positive regulation of cell to cell adhesion.
canonical Wnt signaling pathway involved in positive regulation of wound healing(GO:0044330)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in positive regulation of wound healing.
canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition(GO:0044334)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in the positive regulation of epithelial cell to mesenchymal cell transition.
canonical Wnt signaling pathway involved in neural crest cell differentiation(GO:0044335)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in neural crest cell differentiation.
canonical Wnt signaling pathway involved in negative regulation of apoptotic process(GO:0044336)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in the negative regulation of apoptotic process.
canonical Wnt signaling pathway involved in positive regulation of apoptotic process(GO:0044337)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in the positive regulation of apoptotic process.
canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation(GO:0044338)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in mesenchymal stem cell differentiation.
canonical Wnt signaling pathway involved in osteoblast differentiation(GO:0044339)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in osteoblast differentiation.
canonical Wnt signaling pathway involved in regulation of cell proliferation(GO:0044340)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contributes to modulating the rate or frequency of cell proliferation.
canonical Wnt signaling pathway involved in regulation of type B pancreatic cell proliferation(GO:0044343)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that modulates the rate or frequency of pancreatic B cell proliferation. Pancreatic B cell are cells of the pancreas that secrete insulin.
multi-species biofilm formation(GO:0044399)biological_processA process in which planktonically growing microorganisms of different species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
multi-species biofilm formation on inanimate substrate(GO:0044400)biological_processA process in which microorganisms of different species attach to and grow on an inanimate surface such as a rock or pipe and produce extracellular polymers that facilitate attachment and matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
multi-species biofilm formation in or on host organism(GO:0044401)biological_processA process in which microorganisms of different species attach to and grow in or on a host species, and produce extracellular polymers that facilitate attachment and matrix formation, resulting in a change in the microorganisms' growth rate and gene transcription. The host is defined as the larger of the organisms involved in a symbiotic interaction.
single-species biofilm formation in or on host organism(GO:0044407)biological_processA process in which microorganisms of the same species attach to and grow in or on a host species, and produce extracellular polymers that facilitate attachment and matrix formation, resulting in a change in the microorganisms' growth rate and gene transcription. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Dsc E3 ubiquitin ligase complex(GO:0044695)cellular_componentAn E3 ubiquitin ligase complex localized to the ER and Golgi membrane. In fission yeast comprises Dsc1, 2, 3 and 4. Involved in the processes of fission yeast sre1 (human SREBP) transcriptional activator proteolytic cleavage, the multivesicular body (MVB) pathway, and a post-endoplasmic reticulum pathway for protein catabolism.
viral genome integration into host DNA(GO:0044826)biological_processThe insertion into a host genome of viral DNA, usually by the action of an integrase enzyme. Once integrated, the provirus persists in the host cell and serves as a template for the transcription of viral genes and replication of the viral genome, leading to the production of new viruses.
triplex DNA binding(GO:0045142)molecular_functionInteracting selectively and non-covalently with a DNA triple helix. The formation of triple helical DNA has been evoked in several cellular processes including transcription, replication, and recombination.
antisigma factor binding(GO:0045152)molecular_functionInteracting selectively and non-covalently with an antisigma factor, a factor which inhibits the ability of the sigma factor to function as a transcriptional initiator.
mRNA editing complex(GO:0045293)cellular_componentA protein complex that posttranscriptionally catalyzes insertion, deletion or substitution of nucleotides at multiple sites within nascent mRNA transcripts to produce mature mRNAs in eukaryotes.
sevenless signaling pathway(GO:0045500)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to sevenless (sev; a receptor tyrosine kinase) on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
obsolete regulation of survival gene product expression(GO:0045884)biological_processOBSOLETE. Any process that modulates the frequency, rate or extent of survival gene product expression; survival gene products are those that antagonize the apoptotic program. Regulation can be at the transcriptional, translational, or posttranslational level. This term was made obsolete because the meaning of the term is ambiguous: the same gene product may or may not have a role in apoptosis depending on the cell type, tissue type, condition, etc.
obsolete positive regulation of survival gene product expression(GO:0045885)biological_processOBSOLETE. Any process that activates or increases the frequency, rate or extent of survival gene product expression; survival gene products are those that antagonize the apoptotic program. Regulation can be at the transcriptional, translational, or posttranslational level. This term was made obsolete because the meaning of the term is ambiguous: the same gene product may or may not have a role in apoptosis depending on the cell type, tissue type, condition, etc.
dosage compensation complex(GO:0046536)cellular_componentA protein or protein-RNA complex that localizes to one or more of the sex chromosome(s), where it acts to normalize transcription between different sexes.
replication compartment(GO:0046809)cellular_componentGlobular nuclear domains where the transcription and replication of the viral genome occurs. More than one site can be present simultaneously.
vascular endothelial growth factor receptor signaling pathway(GO:0048010)biological_processAny series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
neurotrophin TRK receptor signaling pathway(GO:0048011)biological_processA series of molecular signals initiated by the binding of a neurotrophin to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
long-term maintenance of gene activation(GO:0048097)biological_processAny mechanism, at the level of transcription or post-transcription, maintaining gene activation in the long-term.
leukemia inhibitory factor signaling pathway(GO:0048861)biological_processAny series of molecular signals initiated by the binding of leukemia inhibitory factor to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
AF-2 domain binding(GO:0050682)molecular_functionInteracting selectively and non-covalently with the AF-2 domain of a protein, a highly conserved ligand-dependent transactivation domain which is essential for receptor-mediated transcriptional activation.
AF-1 domain binding(GO:0050683)molecular_functionInteracting selectively and non-covalently with the AF-1 domain of a protein, a ligand-independent transactivation domain which is required for the full transcriptional activity of the receptor.
NF-kappaB binding(GO:0051059)molecular_functionInteracting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
RNA virus induced gene silencing(GO:0051214)biological_processGene silencing induced by RNA viruses leading to a sequence-specific degradation of target mRNAs or post-transcriptional gene silencing.
DNA virus induced gene silencing(GO:0051215)biological_processGene silencing induced by DNA viruses leading to a sequence-specific degradation of target mRNAs or post-transcriptional gene silencing.
NFAT protein binding(GO:0051525)molecular_functionInteracting selectively and non-covalently with NFAT (nuclear factor of activated T cells) proteins, a family of transcription factors. NFAT proteins have crucial roles in the development and function of the immune system.
canonical Wnt signaling pathway(GO:0060070)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
host cellular process involved in virus induced gene silencing(GO:0060144)biological_processA cellular process occurring in the host cell that contributes to the process of posttranscriptional gene inactivation ('silencing') both of viral gene(s), and host gene(s) homologous to the viral genes.
viral gene silencing in virus induced gene silencing(GO:0060145)biological_processThe posttranscriptional gene silencing of viral genes after viral infection.
host gene silencing in virus induced gene silencing(GO:0060146)biological_processThe posttranscriptional gene silencing of host genes that are homologous to viral genes after viral infection.
viral triggering of virus induced gene silencing(GO:0060150)biological_processAny process that increases the frequency, rate or extent of the inactivation of gene expression of both viral genes and host homologues to those genes by a posttranscriptional mechanism in a virally infected cell.
interferon-gamma-mediated signaling pathway(GO:0060333)biological_processA series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
type I interferon signaling pathway(GO:0060337)biological_processA series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
JAK-STAT cascade involved in growth hormone signaling pathway(GO:0060397)biological_processThe process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.
canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation(GO:0060823)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contributes to the formation of the neural plate anterior/posterior pattern.
regulation of canonical Wnt signaling pathway(GO:0060828)biological_processAny process that modulates the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
regulation of hair cycle by canonical Wnt signaling pathway(GO:0060901)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that modulates the rate, frequency or extent of the hair cycle.
negative regulation of chromatin silencing by small RNA(GO:0060906)biological_processAny process that decreases the frequency, rate or extent of chromatin silencing by small RNA. Chromatin silencing by small RNA is the repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region.
regulation of gene silencing by miRNA(GO:0060964)biological_processAny process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
negative regulation of gene silencing by miRNA(GO:0060965)biological_processAny process that decreases the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
regulation of gene silencing(GO:0060968)biological_processAny process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
negative regulation of gene silencing(GO:0060969)biological_processAny process that decreases the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
negative regulation of chromatin silencing at silent mating-type cassette(GO:0061186)biological_processAny process that decreases the frequency, rate, or extent of chromatin silencing at silent mating-type cassette. Chromatin silencing at silent mating-type cassette is the repression of transcription at silent mating-type loci by altering the structure of chromatin.
regulation of chromatin silencing at rDNA(GO:0061187)biological_processAny process that modulates the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin.
negative regulation of chromatin silencing at rDNA(GO:0061188)biological_processAny process that decreases the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin.
canonical Wnt signaling pathway involved in metanephric kidney development(GO:0061290)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contribute to the progression of the metanephric kidney over time. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
canonical Wnt signaling pathway involved in ureteric bud branching(GO:0061291)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contributes to the branching of the ureteric bud. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
canonical Wnt signaling pathway involved in mesonephros development(GO:0061292)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contributes to the progression of the mesonephros over time. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
canonical Wnt signaling pathway involved in mesonephric nephron development(GO:0061293)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contribute to the progression of the mesonephric nephron over time. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development(GO:0061310)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in cardiac neural crest cell differentiation.
canonical Wnt signaling pathway involved in heart development(GO:0061316)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contributes to the progression of the heart over time. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment(GO:0061317)biological_processThe series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin and contributing to cardiac muscle cell fate commitment. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
interleukin-34-mediated signaling pathway(GO:0061514)biological_processA series of molecular signals initiated by the binding of interleukin-34 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
miRNA 2'-O-methylation(GO:0061715)biological_processThe posttranscriptional addition of a methyl group to the 2' oxygen atom of a nucleotide residue in an miRNA molecule.
leukotriene signaling pathway(GO:0061737)biological_processA series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-leukotriene interaction and ends with regulation of a downstream cellular process, e.g. transcription.
obsolete ARID domain binding(GO:0061813)molecular_functionInteracting selectively and non-covalently with a ARID domain. The AT-rich interaction domain (ARID) is an ~100-amino acid DNA-binding module found in a large number of eukaryotic transcription factors.
Pi Mi complex(GO:0062071)cellular_componentA transcription factor complex composed of a homeodomain protein and the M-specific peptide Mi that acts at the regulatory region of genes required for the activation of meiosis.
tRNA gene clustering(GO:0070058)biological_processThe process in which tRNA genes, which are not linearly connected on the chromosome, are transported in three dimensions to, and maintained together in, the nucleolus. This clustered positioning leads to transcriptional silencing of nearby RNA polymerase II promoters (termed tRNA gene mediated (tgm) silencing) in S. cerevisiae.
chemokine-mediated signaling pathway(GO:0070098)biological_processA series of molecular signals initiated by the binding of a chemokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-6-mediated signaling pathway(GO:0070102)biological_processA series of molecular signals initiated by the binding of interleukin-6 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-27-mediated signaling pathway(GO:0070106)biological_processA series of molecular signals initiated by the binding of interleukin-27 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
ciliary neurotrophic factor-mediated signaling pathway(GO:0070120)biological_processA series of molecular signals initiated by the binding of a ciliary neurotrophic factor (CNTF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
DRM complex(GO:0070176)cellular_componentA transcriptional repressor complex that contains the lin-9, lin-35, lin-37, lin-52, lin-53, lin-5is involved in 4-, dpl-1 and efl-1 proteins, and is involved in cell fate specification.
obsolete proton-transporting ATP synthase complex biogenesis(GO:0070272)biological_processOBSOLETE. The biogenesis of a proton-transporting ATP synthase (also known as F-type ATPase), a two-sector ATPase found in the inner membrane of mitochondria and chloroplasts, and in bacterial plasma membranes. Includes the synthesis of constituent proteins and their aggregation, arrangement and bonding together. The reason for obsoletion is that 'biogenesis' as related to a protein is translation, and there is no indication that the members of these complexes are synthesized in a particular way. Historically biogenesis terms were created for some processes when the level of a molecule was changed by an unknown mechanism, for instance transcription, translation, assembly etc. This is now considered too indirect for annotation. See https://github.com/geneontology/go-ontology/issues/15173
nucleosomal methylation activator complex(GO:0070311)cellular_componentA protein complex that contains eight subunits in common with the SWI/SNF complex, plus the ATPase BRG1 (SMARCA4) and the histone methyltransferase CARM1; the complex is involved in regulating nuclear receptor-dependent transcription.
RGS6-DNMT1-DMAP1 complex(GO:0070313)cellular_componentA protein complex formed by the association of RGS6, a negative regulator of heterotrimeric G protein signaling, with the DMAP1-Dnmt1 transcriptional repressor complex; in the complex, RGS6 inhibits the transcriptional repressor activity of DMAP1.
GATA1-TAL1-TCF3-Lmo2 complex(GO:0070353)cellular_componentA protein complex that contains the zinc finger transcription factor GATA1, the LIM domain protein Lmo2 (RBTN2), the basic helix-loop-helix protein TAL1 and its binding partner TCF3. The complex is involved transcriptional regulation in hematopoiesis.
GATA2-TAL1-TCF3-Lmo2 complex(GO:0070354)cellular_componentA protein complex that contains the zinc finger transcription factor GATA2, the LIM domain protein Lmo2 (RBTN2), the basic helix-loop-helix protein TAL1 and its binding partner TCF3. The complex is involved transcriptional regulation in hematopoiesis.
beta-catenin-TCF7L2 complex(GO:0070369)cellular_componentA protein complex that contains beta-catenin and TCF7L2 (TCF4), binds to the TCF DNA motif within a promoter element, and is involved in the regulation of WNT target gene transcription.
Mad-Max-mSin3A complex(GO:0070439)cellular_componentA transcriptional repressor complex that contains a heterodimer of the bHLH-ZIP proteins Mad and Max, plus mSin3A, a homolog of the yeast Sin3p.
Mad-Max-mSin3B complex(GO:0070440)cellular_componentA transcriptional repressor complex that contains a heterodimer of the bHLH-ZIP proteins Mad and Max, plus mSin3B, a homolog of the yeast Sin3p.
Mad-Max complex(GO:0070443)cellular_componentA transcriptional repressor complex that consists of a heterodimer of the bHLH-ZIP proteins Mad and Max.
interleukin-1-mediated signaling pathway(GO:0070498)biological_processA series of molecular signals initiated by the binding of interleukin-1 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
SRF-myogenin-E12 complex(GO:0070514)cellular_componentA transcription factor complex that contains the serum response factor (SRF) and the basic helix-loop-helix proteins myogenin and E12, and is involved in activating transcription of muscle-specific genes.
juvenile hormone response element binding(GO:0070594)molecular_functionInteracting selectively and non-covalently with the juvenile hormone response element (JHRE), a conserved sequence found in the promoters of genes whose expression is regulated in response to juvenile hormone.
vitamin D response element binding(GO:0070644)molecular_functionInteracting selectively and non-covalently with the vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum.
P-TEFb-cap methyltransferase complex(GO:0070693)cellular_componentA protein complex that is formed by the association of positive transcription elongation factor complex b (P-TEFb) with the mRNA capping methyltransferase.
Tle3-Aes complex(GO:0070722)cellular_componentA transcriptional repressor complex that consists of a heterodimer of the proteins Tle3 (also known as Grg3b) and Aes (Grg5), which are homologs of the Drosophila groucho gene product.
interleukin-35-mediated signaling pathway(GO:0070757)biological_processA series of molecular signals initiated by the binding of interleukin-35 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
phosphorylation of RNA polymerase II C-terminal domain(GO:0070816)biological_processThe process of introducing a phosphate group on to an amino acid residue in the C-terminal domain of RNA polymerase II. Typically, this occurs during the transcription cycle and results in production of an RNA polymerase II enzyme where the carboxy-terminal domain (CTD) of the largest subunit is extensively phosphorylated, often referred to as hyperphosphorylated or the II(0) form. Specific types of phosphorylation within the CTD are usually associated with specific regions of genes, though there are exceptions. The phosphorylation state regulates the association of specific complexes such as the capping enzyme or 3'-RNA processing machinery to the elongating RNA polymerase complex.
core mediator complex(GO:0070847)cellular_componentA protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The core mediator complex has a stimulatory effect on basal transcription, and contains most of the same subdomains as the larger form of mediator complex -- a head domain comprising proteins known in Saccharomyces as Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; and a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p -- but lacks the regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan core mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
RNA polymerase I core factor complex(GO:0070860)cellular_componentA RNA polymerase I-specific transcription factor complex that is required for the transcription of rDNA by RNA polymerase I. In yeast the complex consists of Rrn6p, Rrn7p, and Rrn11p.
E-box binding(GO:0070888)molecular_functionInteracting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues.
mitochondrial tRNA wobble uridine modification(GO:0070899)biological_processThe process in which a uridine in position 34 of a mitochondrial tRNA is post-transcriptionally modified.
mitochondrial tRNA methylation(GO:0070901)biological_processThe posttranscriptional addition of methyl groups to specific residues in a mitochondrial tRNA molecule.
global genome nucleotide-excision repair(GO:0070911)biological_processThe nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
Ddb1-Ckn1 complex(GO:0070912)cellular_componentA heterodimeric nucleotide-excision repair complex that is involved in transcription-coupled repair. The subunits are known as Ddb1 and Ckn1 in S. pombe; Ddb1 contains a motif called the DDB-box that interacts with adaptor proteins for DDB1/cullin 4 ubiquitin ligases.
Ddb1-Wdr21 complex(GO:0070913)cellular_componentA heterodimeric nucleotide-excision repair complex that is involved in transcription-coupled repair. The subunits are known as Ddb1 and Wdr21 in S. pombe; Ddb1 contains a motif called the DDB-box that interacts with adaptor proteins for DDB1/cullin 4 ubiquitin ligases.
dephosphorylation of RNA polymerase II C-terminal domain(GO:0070940)biological_processThe process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form.
POU domain binding(GO:0070974)molecular_functionInteracting selectively and non-covalently with a POU domain of a protein. The POU domain is a bipartite DNA binding domain composed of two subunits separated by a non-conserved region of 15-55 amino acids; it is found in several eukaryotic transcription factors.
antisense RNA transcript catabolic process(GO:0071041)biological_processThe chemical reactions and pathways resulting in the breakdown of antisense transcripts, i.e. transcripts that were produced from the antisense strand of a gene that produces a gene product and which often have a regulatory effect on the transcription of that gene product.
snoRNA polyadenylation(GO:0071050)biological_processThe enzymatic addition of a sequence of adenylyl residues at the 3' end of snoRNA molecule. In eukaryotes, this occurs in conjunction with termination of transcription of precursor snoRNA molecules and may occur post-transcriptionally on incorrectly processed molecules targeted for degradation.
SMAD protein complex(GO:0071141)cellular_componentA protein complex that consists of only SMAD proteins; may be homomeric or heteromeric. Heteromeric complexes act as transcription factors while homomeric complexes exist but are transcriptionally inactive. Hetero- versus homotrimerization is largely enthalpy driven.
homomeric SMAD protein complex(GO:0071142)cellular_componentA protein complex composed of a single type of SMAD family proteins. In the absence of Smad4, phosphorylation of R-SMADs results in their homotrimerization. However, these complexes do not appear to import into the nucleus and are assumed to be transcriptionally inactive.
heteromeric SMAD protein complex(GO:0071144)cellular_componentA protein complex composed of SMAD family proteins, a transcription factor complex which binds to the promoters of target genes and recruits co-activators and histone acetyltransferases, facilitating transcription. Phosphorylation of the non-SMAD4 subunit(s) enables binding of SMAD4 to form heteromeric complexes that enter the nucleus to initiate gene transcription. DNA-binding specificity is conferred by other transcription factors binding to SMAD complexes. Interactions with coactivators or corepressors modulate their transcriptional activity. Can be heterotrimeric or heterodimeric.
TEAD-2 multiprotein complex(GO:0071147)cellular_componentA protein complex that consists of the DNA binding protein TEAD-2 bound to 12 other polypeptides including the transcriptional coactivator YAP, the multi-PDZ domain protein MPDZ (also called MUPP1), a 14-3-3 domain protein, and others.
TEAD-1-YAP complex(GO:0071148)cellular_componentA transcription factor complex that is composed of the DNA binding protein TEAD-1 and the transcriptional coactivator YAP.
TEAD-2-YAP complex(GO:0071149)cellular_componentA transcription factor complex that is composed of the DNA binding protein TEAD-2 and the transcriptional coactivator YAP.
TEAD-3-YAP complex(GO:0071150)cellular_componentA transcription factor complex that is composed of the DNA binding protein TEAD-3 and the transcriptional coactivator YAP.
TEAD-4-YAP complex(GO:0071151)cellular_componentA transcription factor complex that is composed of the DNA binding protein TEAD-4 and the transcriptional coactivator YAP.
NF-kappaB complex(GO:0071159)cellular_componentA protein complex that consists of a homo- or heterodimer of members of a family of structurally related proteins that contain a conserved N-terminal region called the Rel homology domain (RHD). In the nucleus, NF-kappaB complexes act as transcription factors. In unstimulated cells, NF-kappaB dimers are sequestered in the cytoplasm by IkappaB monomers; signals that induce NF-kappaB activity cause degradation of IkappaB, allowing NF-kappaB dimers to translocate to the nucleus and induce gene expression.
MAML2-RBP-Jkappa-ICN1 complex(GO:0071175)cellular_componentA protein complex that consists of the intracellular domain of Notch1 (ICN1), the DNA-binding transcription factor RBP-Jkappa, and the transcriptional coactivator Mastermind-like-2 (MAML2); the complex is involved in transcriptional activation in response to Notch-mediated signaling.
MAML2-RBP-Jkappa-ICN2 complex(GO:0071176)cellular_componentA protein complex that consists of the intracellular domain of Notch2 (ICN2), the DNA-binding transcription factor RBP-Jkappa, and the transcriptional coactivator Mastermind-like-2 (MAML2); the complex is involved in transcriptional activation in response to Notch-mediated signaling.
MAML2-RBP-Jkappa-ICN3 complex(GO:0071177)cellular_componentA protein complex that consists of the intracellular domain of Notch3 (ICN3), the DNA-binding transcription factor RBP-Jkappa, and the transcriptional coactivator Mastermind-like-2 (MAML2); the complex is involved in transcriptional activation in response to Notch-mediated signaling.
MAML2-RBP-Jkappa-ICN4 complex(GO:0071178)cellular_componentA protein complex that consists of the intracellular domain of Notch4 (ICN4), the DNA-binding transcription factor RBP-Jkappa, and the transcriptional coactivator Mastermind-like-2 (MAML2); the complex is involved in transcriptional activation in response to Notch-mediated signaling.
MAML3-RBP-Jkappa-ICN1 complex(GO:0071179)cellular_componentA protein complex that consists of the intracellular domain of Notch1 (ICN1), the DNA-binding transcription factor RBP-Jkappa, and the transcriptional coactivator Mastermind-like-3 (MAML3); the complex is involved in transcriptional activation in response to Notch-mediated signaling.
MAML3-RBP-Jkappa-ICN2 complex(GO:0071180)cellular_componentA protein complex that consists of the intracellular domain of Notch2 (ICN2), the DNA-binding transcription factor RBP-Jkappa, and the transcriptional coactivator Mastermind-like-3 (MAML3); the complex is involved in transcriptional activation in response to Notch-mediated signaling.
MAML3-RBP-Jkappa-ICN3 complex(GO:0071181)cellular_componentA protein complex that consists of the intracellular domain of Notch3 (ICN3), the DNA-binding transcription factor RBP-Jkappa, and the transcriptional coactivator Mastermind-like-3 (MAML3); the complex is involved in transcriptional activation in response to Notch-mediated signaling.
MAML3-RBP-Jkappa-ICN4 complex(GO:0071182)cellular_componentA protein complex that consists of the intracellular domain of Notch4 (ICN4), the DNA-binding transcription factor RBP-Jkappa, and the transcriptional coactivator Mastermind-like-3 (MAML3); the complex is involved in transcriptional activation in response to Notch-mediated signaling.
catenin-TCF7L2 complex(GO:0071664)cellular_componentA protein complex that contains a catenin and TCF7L2 (TCF4), binds to the TCF DNA motif within a promoter element, and is involved in the regulation of WNT target gene transcription.
gamma-catenin-TCF7L2 complex(GO:0071665)cellular_componentA protein complex that contains gamma-catenin and TCF7L2 (TCF4), binds to the TCF DNA motif within a promoter element, and is involved in the regulation of WNT target gene transcription.
obsolete WINAC complex(GO:0071778)cellular_componentOBSOLETE. A SWI/SNF-type complex that directly interacts with the vitamin D receptor (VDR) through the Williams syndrome transcription factor (WSTF), and mediates the recruitment of unliganded VDR to VDR target sites in promoters. The WINAC complex contains at least 13 subunits, including WSTF, several SWI/SNF components, and DNA replication-related factors. This term was made obsolete because the paper describing the characterization of this complex, which was used to create this term, has been retracted.
N-box binding(GO:0071820)molecular_functionInteracting selectively and non-covalently with an N-box, a DNA motif with the consensus sequence CACNAG that is found in the promoters of genes expressed preferentially at synapses.
HMG box domain binding(GO:0071837)molecular_functionInteracting selectively and non-covalently with an HMG box domain, a protein domain that consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin.
TNFSF11-mediated signaling pathway(GO:0071847)biological_processA series of molecular signals initiated by the binding of tumor necrosis factor ligand superfamily member 11 (TNFSF11) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cleavage body(GO:0071920)cellular_componentA nuclear body that contains proteins involved in pre-mRNA 3'-end cleavage and polyadenylation, such as DDX1, CSTF2 and CPSFs, as well as the transcription factors TFIIE and TFIIF. Cleavage bodies are localized adjacent to Cajal bodies and are involved in mRNA3'-end processing.
endocannabinoid signaling pathway(GO:0071926)biological_processThe series of molecular signals generated as a consequence of an endocannabinoid binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription. Endocannabinoids are small molecules derived from arachidonic acid, anandamide (arachidonoylethanolamide) and 2-arachidonoylglycerol.
Myc-Max complex(GO:0071943)cellular_componentA transcription factor complex that consists of a heterodimer of the bHLH-ZIP proteins Myc and Max.
regulation of canonical Wnt signaling pathway involved in neural crest cell differentiation(GO:0072335)biological_processAny process that modulates the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin involved in neural crest cell differentiation. The Wnt signaling pathway is the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
negative regulation of canonical Wnt signaling pathway involved in neural crest cell differentiation(GO:0072336)biological_processAny process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin involved in neural crest cell differentiation. The Wnt signaling pathway is the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
positive regulation of canonical Wnt signaling pathway involved in neural crest cell differentiation(GO:0072381)biological_processAny process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin involved in neural crest cell differentiation. The Wnt signaling pathway is the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
host cell Cajal body(GO:0072495)cellular_componentA class of nuclear body in the eukaryotic host cell, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA. The host is the larger of the organisms involved in a symbiotic interaction.
obsolete chromatin silencing at centromere central core(GO:0072692)biological_processRepression of transcription of DNA at the central core of a regional centromere by altering the structure of chromatin. This term was made obsolete because the process does not exist.
mRNA methylation(GO:0080009)biological_processThe posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.
obsolete chloroplast ribulose bisphosphate carboxylase complex biogenesis(GO:0080158)biological_processOBSOLETE. A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a chloroplast ribulose bisphosphate carboxylase (RubisCO) complex. Includes the synthesis of the constituent protein molecules, and those protein modifications that are involved in synthesis or assembly of the complex. The reason for obsoletion is that 'biogenesis' as related to a protein is translation, and there is no indication that the members of these complexes are synthesized in a particular way. Historically biogenesis terms were created for some processes when the level of a molecule was changed by an unknown mechanism, for instance transcription, translation, assembly etc. This is now considered too indirect for annotation. See https://github.com/geneontology/go-ontology/issues/15173
endothelin receptor signaling pathway(GO:0086100)biological_processA series of molecular signals initiated by an endothelin receptor binding to one of its physiological ligands, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. Ends with regulation of a downstream cellular process, e.g. transcription.
Cbf1-Met4-Met28 complex(GO:0089713)cellular_componentA heteromeric complex consisting of Cbf1 and basic leucine zipper (bZIP) containing transcriptional activators, Met4 and Met28, that forms over the sequence TCACGTG in the upstream activating sequence (UAS) of genes involved in sulfur amino acid metabolism, resulting in their transcriptional activation.
Pip2-Oaf1 complex(GO:0089716)cellular_componentA heterodimeric complex consisting of Zn(2)Cys(6) containing transcription factors Pip2 and Oaf1. It binds to the oleate response element (ORE), found in the promoters of fatty acid-inducible genes in Saccharomyces where, in the presence of oleate this bound complex activates the transcription of genes encoding peroxisomal proteins.
replication fork arrest at tRNA locus(GO:0090001)biological_processA process that impedes the progress of the DNA replication fork at natural replication fork pausing sites within the eukaryotic tRNA transcription unit.
Wnt signaling pathway involved in primitive streak formation(GO:0090011)biological_processThe series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in transcription of target genes that contribute to the formation of the primitive streak.
regulation of chromatin silencing at centromere(GO:0090052)biological_processAny process that modulates the frequency, rate or extent of chromatin silencing at the centromere. Chromatin silencing at the centromere is the repression of transcription of centromeric DNA by altering the structure of chromatin.
positive regulation of chromatin silencing at centromere(GO:0090053)biological_processAny process that increases the frequency, rate or extent of chromatin silencing at the centromere. Chromatin silencing at the centromere is the repression of transcription of centromeric DNA by altering the structure of chromatin.
regulation of chromatin silencing at silent mating-type cassette(GO:0090054)biological_processAny process that modulates the frequency, rate, or extent of chromatin silencing at silent mating-type cassette. Chromatin silencing at silent mating-type cassette is the repression of transcription at silent mating-type loci by altering the structure of chromatin.
positive regulation of chromatin silencing at silent mating-type cassette(GO:0090055)biological_processAny process that increases the frequency, rate, or extent of chromatin silencing at silent mating-type cassette. Chromatin silencing at silent mating-type cassette is the repression of transcription at silent mating-type loci by altering the structure of chromatin.
regulation of heart induction by regulation of canonical Wnt signaling pathway(GO:0090081)biological_processAny process that modulates the rate, frequency or extent of canonical Wnt signaling pathway that regulates heart induction. Canonical Wnt signaling pathway involved in heart induction is the series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell, followed by relaying of the signal via beta-catenin, and ending with a change in transcription of target genes.
positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway(GO:0090082)biological_processAny process that decreases the rate, frequency or extent of canonical Wnt signaling pathway that positively regulates heart induction. Canonical Wnt signaling pathway involved in heart induction is the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
negative regulation of canonical Wnt signaling pathway(GO:0090090)biological_processAny process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
positive regulation of canonical Wnt signaling pathway(GO:0090263)biological_processAny process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
regulation of methylation-dependent chromatin silencing(GO:0090308)biological_processAny process that modulates the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
positive regulation of methylation-dependent chromatin silencing(GO:0090309)biological_processAny process that increases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
negative regulation of methylation-dependent chromatin silencing(GO:0090310)biological_processAny process that decreases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
WICH complex(GO:0090535)cellular_componentAn ISWI complex that contains an ATPase subunit of the ISWI family (specifically SNF2H in mammals, which contain two ISWI homologs) and WSTF (Williams Syndrome Transcription Factor). WICH plays roles in regulation of RNAP I and III transcription and in DNA replication and repair.
NoRC complex(GO:0090536)cellular_componentAn ISWI complex that contains an ATPase subunit of the ISWI family (specifically SNF2H in mammals, which contain two ISWI homologs) and a Tip5 homolog. In mammals, NoRC is involved in regulation of transcription from RNAP I and RNA polymerase III promoters.
CERF complex(GO:0090537)cellular_componentAn ISWI complex that contains an ATPase subunit of the ISWI family (specifically SNF2L in mammals, which contain two ISWI homologs) and a CECR2 homolog. In mammals, CERF is involved in regulation of transcription from RNA polymerase II promoters.
surface biofilm formation(GO:0090604)biological_processA process in which planktonically growing microorganisms grow at the surface of a liquid-air interface and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
submerged biofilm formation(GO:0090605)biological_processA process in which planktonically growing microorganisms aggregate and grow on solid substrates under the flow of a liquid and produce extracellular polymers that facilitate attachment and matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
multi-species surface biofilm formation(GO:0090607)biological_processA process in which planktonically growing microorganisms of different species grow at the surface of a liquid-air interface and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
multi-species submerged biofilm formation(GO:0090608)biological_processA process in which planktonically growing microorganisms of different species aggregate and grow on solid substrates under the flow of a liquid and produce extracellular polymers that facilitate attachment and matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
single-species submerged biofilm formation(GO:0090609)biological_processA process in which planktonically growing microorganisms of the same species aggregate and grow on solid substrates under the flow of a liquid and produce extracellular polymers that facilitate attachment and matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
mitochondrial mRNA processing(GO:0090615)biological_processSteps involved in processing precursor RNAs arising from transcription of operons in the mitochondrial genome into mature mRNAs.
obsolete mitochondrial respiratory chain complex I biogenesis(GO:0097031)biological_processOBSOLETE. The biogenesis of a mitochondrial respiratory chain complex I, a protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Includes the synthesis of constituent proteins and their aggregation, arrangement and bonding together. The reason for obsoletion is that 'biogenesis' as related to a protein is translation, and there is no indication that the members of these complexes are synthesized in a particular way. Historically biogenesis terms were created for some processes when the level of a molecule was changed by an unknown mechanism, for instance transcription, translation, assembly etc. This is now considered too indirect for annotation. See https://github.com/geneontology/go-ontology/issues/15173
obsolete mitochondrial respiratory chain complex II biogenesis(GO:0097032)biological_processOBSOLETE. The biogenesis of a mitochondrial respiratory chain complex II, a protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Includes the synthesis of constituent proteins and their aggregation, arrangement and bonding together. The reason for obsoletion is that 'biogenesis' as related to a protein is translation, and there is no indication that the members of these complexes are synthesized in a particular way. Historically biogenesis terms were created for some processes when the level of a molecule was changed by an unknown mechanism, for instance transcription, translation, assembly etc. This is now considered too indirect for annotation. See https://github.com/geneontology/go-ontology/issues/15173
obsolete mitochondrial respiratory chain complex III biogenesis(GO:0097033)biological_processOBSOLETE. The biogenesis of a mitochondrial respiratory chain complex III (also known as cytochrome bc(1) complex or ubiquinol-cytochrome c reductase), a protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Includes the synthesis of constituent proteins and their aggregation, arrangement and bonding together. The reason for obsoletion is that 'biogenesis' as related to a protein is translation, and there is no indication that the members of these complexes are synthesized in a particular way. Historically biogenesis terms were created for some processes when the level of a molecule was changed by an unknown mechanism, for instance transcription, translation, assembly etc. This is now considered too indirect for annotation. See https://github.com/geneontology/go-ontology/issues/15173
obsolete mitochondrial respiratory chain complex IV biogenesis(GO:0097034)biological_processOBSOLETE. The biogenesis of a mitochondrial respiratory chain complex IV (also known as cytochrome c oxidase complex), a protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Includes the synthesis of constituent proteins and their aggregation, arrangement and bonding together. The reason for obsoletion is that 'biogenesis' as related to a protein is translation, and there is no indication that the members of these complexes are synthesized in a particular way. Historically biogenesis terms were created for some processes when the level of a molecule was changed by an unknown mechanism, for instance transcription, translation, assembly etc. This is now considered too indirect for annotation. See https://github.com/geneontology/go-ontology/issues/15173
supercoiled DNA binding(GO:0097100)molecular_functionInteracting selectively and non-covalently with supercoiled DNA. For example, during replication and transcription, template DNA is negatively supercoiled in the receding downstream DNA and positively supercoiled in the approaching downstream DNA.
MADS box domain binding(GO:0097162)molecular_functionInteracting selectively and non-covalently with a MADS box domain, a protein domain that encodes the DNA-binding MADS domain. The MADS domain binds to DNA sequences of high similarity to the motif CC[A/T]6GG termed the CArG-box. MADS-domain proteins are generally transcription factors. The length of the MADS-box is in the range of 168 to 180 base pairs.
INO80-type complex(GO:0097346)cellular_componentA chromatin remodeling protein complex initially purified from S. cerevisiae and containing more than 10 subunits, including the SWR1-related complexes. INO80 (inositol requiring 80)-type complexes have diverse functions, including promoting transcriptional activation and DNA repair.
interleukin-32-mediated signaling pathway(GO:0097399)biological_processA series of molecular signals initiated by the binding of interleukin-32 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
interleukin-17-mediated signaling pathway(GO:0097400)biological_processA series of molecular signals initiated by the binding of interleukin-17 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
hypoxia-inducible factor-1alpha signaling pathway(GO:0097411)biological_processA series of molecular signals mediated by hypoxia-inducible factor (HIF1) in response to lowered oxygen levels (hypoxia). Under hypoxic conditions, the oxygen-sensitive alpha-subunit of hypoxia-inducible factor (HIF)-1 dimerizes with a HIF1-beta subunit (also called ARNT or aryl-hydrocarbon-receptor nuclear translocator), translocates to the nucleus and activates transcription of genes whose products participate in responding to hypoxia.
H-NS-Hha complex(GO:0097495)cellular_componentA trimeric protein complex made up of an H-NS homodimer and an Hha monomer. In Enterobacteriaceae, this complex negatively regulates transcription of a range of genes.
necroptotic signaling pathway(GO:0097527)biological_processA series of molecular signals which triggers the necroptotic death of a cell. The pathway starts with reception of a signal, is characterized by activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3, also called RIP1/3), and ends when the execution phase of necroptosis is triggered.
STAT cascade(GO:0097696)biological_processAn intracellular signal transduction process in which STAT proteins (Signal Transducers and Activators of Transcription) convey a signal to trigger a change in the activity or state of a cell. The STAT cascade begins with activation of STAT proteins by kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins.
calcineurin-mediated signaling(GO:0097720)biological_processAny intracellular signal transduction in which the signal is passed on within the cell by activation of a transcription factor as a consequence of dephosphorylation by Ca(2+)-activated calcineurin. The process begins with calcium-dependent activation of the phosphatase calcineurin. Calcineurin is a calcium- and calmodulin-dependent serine/threonine protein phosphatase with a conserved function in eukaryotic species from yeast to humans. In yeast and fungi, calcineurin regulates stress signaling and cell cycle, and sporulation and virulence in pathogenic fungi. In metazoans, calcineurin is involved in cell commitment, organogenesis and organ development and immune function of T-lymphocytes. By a conserved mechanism, calcineurin phosphatase activates fungal Crz1 and mammalian NFATc by dephosphorylation and translocation of these transcription factors to the nucleus to regulate gene expression.
NMDA selective glutamate receptor signaling pathway(GO:0098989)biological_processA series of molecular signals initiated by glutamate binding to an NMDA-selective glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
AMPA selective glutamate receptor signaling pathway(GO:0098990)biological_processA series of molecular signals initiated by glutamate binding to an AMPA-selective glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
kainate selective glutamate receptor signaling pathway(GO:0098991)biological_processA series of molecular signals initiated by glutamate binding to an kainate-selective glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
activating signal cointegrator 1 complex(GO:0099053)cellular_componentA protein complex that contains TRIP4 (ASC1) and acts a transcriptional coactivator by interacting with transcription factors such as NF-kappa B. In humans this complex has 4 subunits: TRIP4 + ASCC1-3.
chromatin silencing at subtelomere(GO:0099114)biological_processRepression of transcription of subtelomeric DNA by altering the structure of chromatin.
presynapse to nucleus signaling pathway(GO:0099526)biological_processA series of molecular signals that conveys information from the presynapse to the nucleus via cytoskeletal transport of a protein from a presynapse to the component to the nucleus where it affects biochemical processes that occur in the nucleus (e.g DNA transcription, mRNA splicing, or DNA/histone modifications).
postsynapse to nucleus signaling pathway(GO:0099527)biological_processA series of molecular signals that conveys information from the postsynapse to the nucleus via cytoskeletal transport of a protein from a postsynapse to the component to the nucleus where it affects biochemical processes that occur in the nucleus (e.g DNA transcription, mRNA splicing, or DNA/histone modifications).
toxin-antitoxin complex(GO:0110001)cellular_componentA bacterial protein complex that neutralises its own toxin by complexing the toxin with the antitoxin. The antitoxin can be either a protein or an RNA. The neutralising toxin-antitoxin complex also acts as a transcriptional repressor of the toxin-antitoxin operon.
B-WICH complex(GO:0110016)cellular_componentA chromatin remodeling complex that positively regulates histone H3 acetylation, in particular H3K9, by recruiting histone acetyltransferases to rDNA gene regions. Located in the nucleolus where it assembles on RNA Polymerase I (Pol I) and possibly on RNA Polymerase III (Pol III) promoter and coding regions during early G1 phase and activates the post-initiation phases of Pol I transcription. May also activate RNA Polymerase II (Pol II) gene transcription. In mammals, B-WICH contains the WICH complex core of BAZ1B and SMARCA5, additional protein subunits and possibly rRNAs. Although it contains several catalytic subunits it is not clear which functions are carried out by the complex itself.
RNA polymerase II termination complex(GO:0110103)cellular_componentA conserved protein complex capable of 5'-3' exoribonuclease activity. It is able to promote RNA polymerase II (RNAPII) transcription termination by degrading pre-mRNA from the newly formed 5' phosphorylated end.
snRNA (adenine-N6)-methylation(GO:0120049)biological_processThe posttranscriptional N6-methylation of an adenine residue in an snRNA molecule.
interleukin-10-mediated signaling pathway(GO:0140105)biological_processA series of molecular signals initiated by the binding of interleukin-10 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
serotonin-gated cation-selective signaling pathway(GO:0140227)biological_processA series of molecular signals initiated by serotonin binding to a seratonin receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
BCOR complex(GO:0140261)cellular_componentA protein-containing complex that monoubiquitinates histone H2A on K119, thus it facilitates the maintenance of the transcriptionally repressive state of some genes, such as BCL6. It consists of the corepressor BCOR or BCORL1, a Polycomb group (PcG) and a SCF ubiquitin ligase subcomplexes.nIn mammals, the core subunits of the complex include the PcG and PcG-associated proteins NSPC1, RING1, RNF2, and RYBP and the components of the SCF ubiquitin ligase, SKP1, and FBXL10.
transforming growth factor beta receptor signaling pathway involved in regulation of multicellular organism growth(GO:1901048)biological_processA series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription, that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
gene expression involved in extracellular matrix organization(GO:1901148)biological_processAny gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form.
obsolete tRNA methylation in response to nitrogen starvation(GO:1901619)biological_processOBSOLETE The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule as a result of deprivation of nitrogen.
regulation of melanosome organization(GO:1903056)biological_processAny process that modulates the frequency, rate or extent of melanosome organization.
negative regulation of melanosome organization(GO:1903057)biological_processAny process that stops, prevents or reduces the frequency, rate or extent of melanosome organization.
positive regulation of melanosome organization(GO:1903058)biological_processAny process that activates or increases the frequency, rate or extent of melanosome organization.
chromatin silencing at centromere outer repeat region(GO:1990141)biological_processRepression of transcription of DNA at the outer repeat region of a regional centromere by altering the structure of chromatin.
ModE complex(GO:1990198)cellular_componentA dimeric protein complex containing two ModE subunits. Binds directly to DNA to regulate transcription, and is involved in (positively and negatively) regulating various aspects of molybdenum metabolism.
STING complex(GO:1990231)cellular_componentA protein dimer containing two STING monomers. It binds cyclic purine di-nucleotides. Activation of the sting complex by 2',5'-3'-5'-cyclic GMP-AMP activates nuclear transcription factor kB (NF-kB) and interferon regulatory factor 3 (IRF3) which then induce transcription of the genes encoding type I IFN and cytokines active in the innate immune response.
atf1-pcr1 complex(GO:1990243)cellular_componentA heterodimeric transcription factor complex composed of the bZIP proteins atf1 and pcr1. The heterodimer binds m26 sites (homologous to CRE).
anti-Mullerian hormone signaling pathway(GO:1990262)biological_processA series of molecular signals initiated by the binding of anti-Mullerian hormone to its receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
Bre1-Rad6 ubiquitin ligase complex(GO:1990302)cellular_componentA ubiquitin ligase complex consisting of Bre1 and Rad6 that mediates monoubiquitination of histone H2B to form H2BK123ub1. H2BK123ub1 gives a specific tag for epigenetic transcriptional activation, elongation by RNA polymerase II, telomeric silencing, and is also a prerequisite for H3K4me and H3K79me formation. It thereby plays a central role in histone code and gene regulation. It also modulates the formation of double-strand breaks during meiosis.
MUB1-RAD6-UBR2 ubiquitin ligase complex(GO:1990304)cellular_componentA ubiquitin ligase complex consisting of MUB1, RAD6 and UBR2 components. It ubiquitinates, and targets for destruction, the RPN4 transcription factor, which upregulates the proteasome genes. The binding of MUB1 may position the RPN4 ubiquitylation site proximal to the Ubiquitin-RAD6 thioester and allow the transfer of Ubiquitin from RAD6 to RPN4. One of its components, MUB1, is a short-lived protein ubiquitinated by the UBR2-RAD6 ubiquitin conjugating enzyme.
Ire1 complex(GO:1990332)cellular_componentA type-I transmembrane protein complex located in the endoplasmic reticulum (ER) consisting of an IRE1-IRE1 dimer, which forms in response to the accumulation of unfolded protein in the ER. The dimeric complex has endoribonuclease (RNase) activity and evokes the unfolded protein response (UPR) by cleaving an intron of a mRNA coding for the transcription factor HAC1 in yeast or XBP1 in mammals; the complex cleaves a single phosphodiester bond in each of two RNA hairpins (with non-specific base paired stems and loops of consensus sequence CNCNNGN, where N is any base) to remove an intervening intron from the target transcript.
upstream stimulatory factor complex(GO:1990378)cellular_componentA protein complex capable of sequence-specific DNA binding RNA polymerase II transcription factor activity through binding to a symmetrical DNA sequence (E-boxes) (5'-CACGTG-3'). Found in a variety of viral and cellular promoters.
snRNA 2'-O-methylation(GO:1990437)biological_processThe posttranscriptional addition of a methyl group to the 2' oxygen atom of a nucleotide residue in an snRNA molecule.
U6 2'-O-snRNA methylation(GO:1990438)biological_processThe posttranscriptional addition a methyl group to the 2'-oxygen atom of a nucleotide residue in an U6 snRNA molecule.
nucleosome disassembly/reassembly complex(GO:1990453)cellular_componentA protein complex involved in the disassembly and subsequent reassembly of nucleosomes. It associates with the coding region of transcriptionally active genes where it interacts with the RNA polymerase II and affects its processivity during co-transcriptional RNA processing and maturation. It exists as a functionally independent part of the NuA4 complex.
Rhino-Deadlock-Cutoff Complex(GO:1990469)cellular_componentProtein complex found in Drosophila consisting of the gene products of cuff, del and rhi. It regulates the licensing of transcription of dual-strand PIWI interacting RNA (piRNA) source loci by binding to dual-strand-cluster chromatin, probably via the H3K9me3-binding activity of Rhi. Rhi binding brings the putative termination cofactor Cuff in close proximity to the nascent piRNA precursor transcript which it appears to protect from degradation.
piRNA uni-strand cluster binding(GO:1990471)molecular_functionInteracting selectively and non-covalently with uni-strand piRNA clusters, double-stranded DNA regions that give rise to PIWI-interacting RNAs (piRNAs) that map predominantly to only one strand and exhibit hallmarks of canonical Pol II transcription. Uni-strand piRNA clusters are found in many taxa.
piRNA dual-strand cluster binding(GO:1990472)molecular_functionInteracting selectively and non-covalently with dual-strand piRNA clusters, double-stranded DNA regions that give rise to PIWI-interacting RNAs (piRNAs) where piRNAs originate from both DNA strands via noncanonical transcription.
Cry-Per complex(GO:1990512)cellular_componentNuclear transcriptional repressor complex that is capable of negatively regulating CLOCK-BMAL-dependent transactivation of genes in a delayed negative feedback manner which generates circadian rhythms.
Ste12p-Dig1p-Dig2p complex(GO:1990526)cellular_componentA multiprotein complex that is involved in the transcription regulation of mating genes in the yeast S. cerevisiae.
Tec1p-Ste12p-Dig1p complex(GO:1990527)cellular_componentA multiprotein complex that is involved in the transcriptional regulation of primarily filamentation genes, but also mating genes, in the yeast S. cerevisiae.
CHOP-ATF4 complex(GO:1990617)cellular_componentA heterodimeric transcription factor complex that is composed of CHOP (C/EBP homology protein, GADD153) and ATF4 (activating transcription factor 4, also known as cAMP response element binding protein-2/CREB-2) subunits.
CHOP-ATF3 complex(GO:1990622)cellular_componentA heterodimeric protein complex that is composed of CHOP (C/EBP homology protein, GADD153) and ATF3 (activating transcription factor 3) subunits.
obsolete Sigma-E factor negative regulation complex(GO:1990628)cellular_componentOBSOLETE. A protein complex consisting of RseA, RseB and RpoE. It form the inactive form of the sigma-E transcription factor. In response to stress, outer membrane proteins accumulate in the periplasm and activate cleavage of RseA periplasmic domain by DegS, triggering a proteolytic cascade that frees sigma-E to activate gene expression. RseB binding to RseA prevents activated DegS from cleaving RseA. Sigma-E-mediated envelope stress response is the major pathway to ensure homeostasis in the envelope compartment of the cell. This term was obsoleted at the TermGenie Gatekeeper stage.
Nkx-2.5 complex(GO:1990664)cellular_componentA transcription factor complex formed by two or more subunits of Nkx-2.5. Nkx-2.5 is an evolutionary conserved transcription factor important for the specification and differentiation of cardiomyocytes during heart development. It is also required for spleen development. It binds DNA either as a monomer, or a homodimer, or a heterodimer complex to activate or inhibit expression of genes.
Beta-catenin-ICAT complex(GO:1990711)cellular_componentTranscription factor complex that inhibits binding of Tcf to beta-catenin while preserving interaction of catenin with cadherin thus inhibiting transcription mediated by beta-catenin-Tcf complex.
HFE-transferrin receptor complex(GO:1990712)cellular_componentA protein complex containing at least HFE and a transferrin receptor (either TFR1/TFRC or TFR2), proposed to play a role in the sensing of transferrin-bound Fe (Fe2-Tf) on the plasma membrane to regulate hepcidin transcription.
primary miRNA methylation(GO:1990744)biological_processThe posttranscriptional addition of methyl groups to specific residues in an primary miRNA molecule.
GLI-SUFU complex(GO:1990788)cellular_componentA protein repressing GLI's transcription factor activity when SMO signalling is inactive. Upon ligand binding to the upstream receptor PTC (Patched) GLI dissociates from SUFU and activates transcription of hedgehog-target genes. In mammals it consists of SUFU and one of the GLI family proteins.
mitochondrial tRNA wobble position uridine thiolation(GO:1990799)biological_processThe process in which a uridine residue at position 34 in the anticodon of a mitochondrial tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from cysteine to position C2 by several steps.
ligand-gated ion channel signaling pathway(GO:1990806)biological_processA series of molecular signals initiated by activation of a ligand-gated ion channel on the surface of a cell. The pathway begins with binding of an extracellular ligand to a ligand-gated ion channel and ends with a molecular function that directly regulates a downstream cellular process, e.g. transcription.
RNA acetylation(GO:1990884)biological_processThe posttranscriptional addition of one or more acetyl groups to specific residues in an RNA molecule.
beta-catenin-TCF complex(GO:1990907)cellular_componentA protein complex that contains beta-catenin and a member of the T-cell factor (TCF)/lymphoid enhancer binding factor (LEF) family of transcription factors.
Wnt signalosome(GO:1990909)cellular_componentA multiprotein protein complex containing membrane-localized Wnt receptors and cytosolic protein complexes, which is capable of transmitting the Wnt signal. Contains at least a Wnt protein, LRP5 or LRP6, a member of the Frizzled (Fz) family, Axin and and a Dishevelled (DVL) protein.

 

Click on the GO term name to get the PDB entries for which a UniProt entry annotated with this GO term is available. This covers the query level and all lower hierarchical levels.

Click on the GO accession number to get a tree view of the GO hierarchy without information on PDB entries. In this case your query level and all levels of higher hierarchy up to the root level Gene_Ontology (GO:0003673) are displayed.

If you enter the GO tree somewhere and if you want to get a view of the whole tree first click on the GO name. This yields the low-hierarchy part. Then click on the GO accession number of the lowest hierarchical level. This gives a view of the complete tree. Note, that certain GO terms belong to more than one path.

GO2PDB@JenaLib
Tue Jul 9 10:48:17 2019