BP

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.

TAS

BP

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.

TAS

BP

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.

TAS

BP

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.

TAS

BP

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.

IBA

BP

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.

TAS

BP

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.

TAS

BP

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.

TAS

BP

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.

TAS

BP

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.

TAS

BP

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.

IMP

BP

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).

TAS

BP

GO:0006471

protein ADP-ribosylation

The transfer, from NAD, of ADP-ribose to protein amino acids.

IDA

BP

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.

IMP

BP

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.

IMP

BP

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.

IEA

BP

GO:0010332

response to gamma radiation

Any 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 a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.

IEA

BP

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.

ISS

BP

GO:0010990

regulation of SMAD protein complex assembly

Any process that modulates the rate, frequency, or extent of SMAD protein complex assembly. SMAD protein complex assembly is the aggregation, arrangement and bonding together of a set of components to form a protein complex that contains SMAD proteins.

IEA

BP

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.

IEA

BP

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.

TAS

BP

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.

IEA

BP

GO:0030225

macrophage differentiation

The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.

TAS

BP

GO:0032042

mitochondrial DNA metabolic process

The chemical reactions and pathways involving mitochondrial DNA.

IMP

BP

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.

IDA

BP

GO:0033148

positive regulation of intracellular estrogen receptor signaling pathway

Any process that activates or increases the frequency, rate or extent of the activity of an intracellular estrogen receptor signaling pathway.

IEA

BP

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.

TAS

BP

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.

IMP

BP

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).

IMP

BP

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.

IEA

BP

GO:0043504

mitochondrial DNA repair

The process of restoring mitochondrial DNA after damage.

IMP

BP

GO:0044030

regulation of DNA methylation

Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.

IEA

BP

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.

IEA

BP

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.

IBA

BP

GO:0051901

positive regulation of mitochondrial depolarization

Any process that activates, maintains or increases the frequency, rate or extent of the change in the membrane potential of the mitochondria from negative to positive.

IEA

BP

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.

IEA

BP

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.

IDA

BP

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.

TAS

BP

GO:0071294

cellular response to zinc ion

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 zinc ion stimulus.

IEA

BP

GO:1901216

positive regulation of neuron death

Any process that activates or increases the frequency, rate or extent of neuron death.

IEA

BP

GO:1903376

regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway

Any process that modulates the frequency, rate or extent of oxidative stress-induced neuron intrinsic apoptotic signaling pathway.

IEA

BP

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.

IMP

BP

GO:1904044

response to aldosterone

Any 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 an aldosterone stimulus.

IEA

BP

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.

ISS

BP

GO:1904646

cellular response to beta-amyloid

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 beta-amyloid stimulus.

IEA

BP

GO:1904762

positive regulation of myofibroblast differentiation

Any process that activates or increases the frequency, rate or extent of myofibroblast differentiation.

IEA

BP

GO:1990966

ATP generation from poly-ADP-D-ribose

The process of generating ATP in the nucleus from poly-ADP-D-ribose. Nuclear ATP generation is required for extensive chromatin remodeling events that are energy-consuming.

IDA

BP

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.

IEA

CC

GO:0000784

nuclear chromosome, telomeric region

The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.

IDA

CC

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.

IDA

CC

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).

IDA

CC

GO:0005654

nucleoplasm

That part of the nuclear content other than the chromosomes or the nucleolus.

TAS

CC

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.

IDA

CC

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.

IDA

CC

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.

IDA

CC

GO:0016020

membrane

A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

IDA

CC

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.

IDA

MF

GO:0003677

DNA binding

Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

IEA

MF

GO:0003910

DNA ligase (ATP) activity

Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m).

IBA

MF

GO:0003950

NAD+ ADP-ribosyltransferase activity

Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.

IDA|TAS

MF

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).

IPI

MF

GO:0008134

transcription factor binding

Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.

IPI

MF

GO:0008270

zinc ion binding

Interacting selectively and non-covalently with zinc (Zn) ions.

IEA

MF

GO:0019899

enzyme binding

Interacting selectively and non-covalently with any enzyme.

IPI

MF

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.

IPI

MF

GO:0030331

estrogen receptor binding

Interacting selectively and non-covalently with an estrogen receptor.

IEA

MF

GO:0042826

histone deacetylase binding

Interacting selectively and non-covalently with the enzyme histone deacetylase.

IEA

MF

GO:0044822

poly(A) RNA binding

Interacting non-covalently with a poly(A) RNA, a RNA molecule which has a tail of adenine bases.

IDA

MF

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.

IPI

MF

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.

IEA

MF

GO:0070412

R-SMAD binding

Interacting selectively and non-covalently with a receptor-regulated SMAD signaling protein.

IEA