| molecular function |
|---|
| | GO:0003677 | | DNA binding | | Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). |
| | GO:0003910 | | DNA ligase (ATP) activity | | Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m). |
| | GO:0051287 | | NAD binding | | Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH. |
| | GO:0003950 | | NAD+ ADP-ribosyltransferase activity | | Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor. |
| | GO:0070412 | | R-SMAD binding | | Interacting selectively and non-covalently with a receptor-regulated SMAD signaling protein. |
| | GO:0019899 | | enzyme binding | | Interacting selectively and non-covalently with any enzyme. |
| | GO:0042826 | | histone deacetylase binding | | Interacting selectively and non-covalently with the enzyme histone deacetylase. |
| | GO:0042802 | | identical protein binding | | Interacting selectively and non-covalently with an identical protein or proteins. |
| | GO:0046872 | | metal ion binding | | Interacting selectively and non-covalently with any metal ion. |
| | GO:0047485 | | protein N-terminus binding | | Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue. |
| | GO:0005515 | | protein binding | | Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). |
| | GO:0019901 | | protein kinase binding | | Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. |
| | GO:0008134 | | transcription factor binding | | Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription. |
| | GO:0016740 | | transferase activity | | Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. |
| | GO:0016757 | | transferase activity, transferring glycosyl groups | | Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor). |
| | GO:0008270 | | zinc ion binding | | Interacting selectively and non-covalently with zinc (Zn) ions. |
| biological process |
|---|
| | GO:0042769 | | DNA damage response, detection of DNA damage | | The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal. |
| | GO:0051103 | | DNA ligation involved in DNA repair | | The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair. |
| | GO:0006281 | | DNA repair | | The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. |
| | GO:0006974 | | cellular response to DNA damage stimulus | | Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. |
| | GO:0032869 | | cellular response to insulin stimulus | | Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms. |
| | GO:0034599 | | cellular response to oxidative stress | | Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of 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. |
| | GO:0006302 | | double-strand break repair | | The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix. |
| | GO:0000724 | | double-strand break repair via homologous recombination | | The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule. |
| | GO:0070911 | | global genome nucleotide-excision repair | | The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome. |
| | GO:0006273 | | lagging strand elongation | | The synthesis of DNA from a template strand in a net 3' to 5' direction. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork. |
| | GO:0030225 | | macrophage differentiation | | The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage. |
| | GO:0032042 | | mitochondrial DNA metabolic process | | The chemical reactions and pathways involving mitochondrial DNA. |
| | GO:0043504 | | mitochondrial DNA repair | | The process of restoring mitochondrial DNA after damage. |
| | GO:0007005 | | mitochondrion organization | | A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components. |
| | GO:1904357 | | negative regulation of telomere maintenance via telomere lengthening | | Any process that stops, prevents or reduces the frequency, rate or extent of telomere maintenance via telomere lengthening. |
| | GO:0000122 | | negative regulation of transcription from RNA polymerase II promoter | | Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. |
| | GO:0000715 | | nucleotide-excision repair, DNA damage recognition | | The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix. |
| | GO:0000717 | | nucleotide-excision repair, DNA duplex unwinding | | The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage. |
| | GO:0033683 | | nucleotide-excision repair, DNA incision | | A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. |
| | GO:0006295 | | nucleotide-excision repair, DNA incision, 3'-to lesion | | The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage. |
| | GO:0006296 | | nucleotide-excision repair, DNA incision, 5'-to lesion | | The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage. |
| | GO:0006294 | | nucleotide-excision repair, preincision complex assembly | | The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage. |
| | GO:0006293 | | nucleotide-excision repair, preincision complex stabilization | | The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage. |
| | GO:0060391 | | positive regulation of SMAD protein import into nucleus | | Any process that increases the rate, frequency or extent of SMAD protein import into the nucleus, i.e. the directed movement of a SMAD proteins from the cytoplasm into the nucleus. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways. |
| | GO:0010613 | | positive regulation of cardiac muscle hypertrophy | | Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division. |
| | GO:0045944 | | positive regulation of transcription from RNA polymerase II promoter | | Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. |
| | GO:2000679 | | positive regulation of transcription regulatory region DNA binding | | Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding. |
| | GO:0006471 | | protein ADP-ribosylation | | The transfer, from NAD, of ADP-ribose to protein amino acids. |
| | GO:0016540 | | protein autoprocessing | | Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein. |
| | GO:0036211 | | protein modification process | | The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). |
| | GO:0070212 | | protein poly-ADP-ribosylation | | The transfer of multiple ADP-ribose residues from NAD to a protein amino acid, forming a poly(ADP-ribose) chain. |
| | GO:0016925 | | protein sumoylation | | The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein. |
| | GO:1903827 | | regulation of cellular protein localization | | Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. |
| | GO:0006355 | | regulation of transcription, DNA-templated | | Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. |
| | GO:0023019 | | signal transduction involved in regulation of gene expression | | Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another. |
| | GO:0006366 | | transcription from RNA polymerase II promoter | | The 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). |
| | GO:0006351 | | transcription, DNA-templated | | The cellular synthesis of RNA on a template of DNA. |
| | GO:0007179 | | transforming growth factor beta receptor signaling pathway | | A 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. |
| cellular component |
|---|
| | GO:0016020 | | membrane | | A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. |
| | GO:0005739 | | mitochondrion | | A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. |
| | GO:0000784 | | nuclear chromosome, telomeric region | | The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins. |
| | GO:0005635 | | nuclear envelope | | The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). |
| | GO:0005730 | | nucleolus | | A 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. |
| | GO:0005654 | | nucleoplasm | | That part of the nuclear content other than the chromosomes or the nucleolus. |
| | GO:0005634 | | nucleus | | A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. |
| | GO:0043234 | | protein complex | | A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. |
| | GO:0005667 | | transcription factor complex | | A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription. |
Description
