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.

IDA

BP

GO:0001837

epithelial to mesenchymal transition

A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.

IMP

BP

GO:0002062

chondrocyte differentiation

The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.

IDA

BP

GO:0003131

mesodermal-endodermal cell signaling

Any process that mediates the transfer of information from mesodermal cells to endodermal cells.

IMP

BP

GO:0006284

base-excision repair

In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.

IDA

BP

GO:0006325

chromatin organization

Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.

TAS

BP

GO:0006355

regulation of transcription, DNA-templated

Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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).

IEA

BP

GO:0007067

mitotic nuclear division

A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.

IEA

BP

GO:0007095

mitotic G2 DNA damage checkpoint

A mitotic cell cycle checkpoint that detects and negatively regulates progression through the G2/M transition of the cell cycle in response to DNA damage.

IDA

BP

GO:0007275

multicellular organism development

The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).

TAS

BP

GO:0009615

response to virus

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 stimulus from a virus.

IEP

BP

GO:0010564

regulation of cell cycle process

Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.

IDA

BP

GO:0010628

positive regulation of gene expression

Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.

IDA

BP

GO:0030261

chromosome condensation

The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.

IEA

BP

GO:0031052

chromosome breakage

Regulated cleavage of the developing macronuclear genome at a limited number of chromosome breakage sites (CBS). The macronuclear destined segment (MDS) sequence adjacent to the CBS (or separated from it by a BES) receives a macronuclear telomere following chromosome breakage.

IDA

BP

GO:0031507

heterochromatin assembly

The assembly of chromatin into heterochromatin, a compact and highly condensed form that is often, but not always, transcriptionally silent.

IDA

BP

GO:0035978

histone H2A-S139 phosphorylation

The modification of histone H2A by the addition of an phosphate group to a serine residue at position 139 of the histone.

IDA

BP

GO:0035986

senescence-associated heterochromatin focus assembly

The 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.

IDA

BP

GO:0035987

endodermal cell differentiation

The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.

IMP

BP

GO:0035988

chondrocyte proliferation

The multiplication or reproduction of chondrocytes by cell division, resulting in the expansion of their population. A chondrocyte is a polymorphic cell that forms cartilage.

IDA

BP

GO:0040008

regulation of growth

Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.

IEA

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.

IDA

BP

GO:0043065

positive regulation of apoptotic process

Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.

IDA

BP

GO:0043066

negative regulation of apoptotic process

Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.

IDA

BP

GO:0043392

negative regulation of DNA binding

Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).

IDA

BP

GO:0043922

negative regulation by host of viral transcription

Any process in which a host organism stops, prevents, or reduces the frequency, rate or extent of viral transcription.

IDA

BP

GO:0045444

fat cell differentiation

The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat.

IMP

BP

GO:0045869

negative regulation of single stranded viral RNA replication via double stranded DNA intermediate

Any process that stops, prevents, or reduces the frequency, rate or extent of single stranded viral RNA replication via double stranded DNA intermediate.

IDA

BP

GO:0045892

negative regulation of transcription, DNA-templated

Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.

IDA|IMP

BP

GO:0045893

positive regulation of transcription, DNA-templated

Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.

IDA|IMP

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.

IDA

BP

GO:0048333

mesodermal cell differentiation

The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell.

IMP

BP

GO:0048762

mesenchymal cell differentiation

The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.

IMP

BP

GO:0048863

stem cell differentiation

The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.

IEP

BP

GO:0051301

cell division

The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.

IEA

BP

GO:0071158

positive regulation of cell cycle arrest

Any process that increases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.

IDA

BP

GO:0090402

oncogene-induced cell senescence

A cellular senescence process associated with the dismantling of a cell as a response to oncogenic stress, such as the activation of the Ras oncogenic family.

IDA

BP

GO:2000036

regulation of stem cell population maintenance

Any process that modulates the frequency, rate or extent of stem cell population maintenance.

IMP|TAS

BP

GO:2000648

positive regulation of stem cell proliferation

Any process that activates or increases the frequency, rate or extent of stem cell proliferation.

IDA|IMP

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.

IDA

BP

GO:2000685

positive regulation of cellular response to X-ray

Any process that activates or increases the frequency, rate or extent of cellular response to X-ray.

IDA

BP

GO:2000774

positive regulation of cellular senescence

Any process that activates or increases the frequency, rate or extent of cellular senescence.

IMP

BP

GO:2001022

positive regulation of response to DNA damage stimulus

Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus.

IDA

BP

GO:2001033

negative regulation of double-strand break repair via nonhomologous end joining

Any process that stops, prevents or reduces the frequency, rate or extent of double-strand break repair via nonhomologous end joining.

IDA

BP

GO:2001038

regulation of cellular response to drug

Any process that modulates the frequency, rate or extent of cellular response to drug.

IDA

CC

GO:0000228

nuclear chromosome

A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.

ISS

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:0005654

nucleoplasm

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

IDA|TAS

CC

GO:0032993

protein-DNA complex

A macromolecular complex containing both protein and DNA molecules.

IDA

CC

GO:0035985

senescence-associated heterochromatin focus

A 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.

IDA

CC

GO:0071141

SMAD protein complex

A protein complex that consists of SMAD proteins; may be homomeric or heteromeric.

IDA

MF

GO:0000975

regulatory region DNA binding

Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair.

IDA

MF

GO:0000989

transcription factor activity, transcription factor binding

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.

IDA

MF

GO:0001047

core promoter binding

Interacting 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.

IDA

MF

GO:0001077

transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding

Interacting 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 activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.

IDA

MF

GO:0001078

transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding

Interacting 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 stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.

IDA

MF

GO:0003677

DNA binding

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

NAS

MF

GO:0003680

AT DNA binding

Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA).

IDA|IMP

MF

GO:0003906

DNA-(apurinic or apyrimidinic site) lyase activity

Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.

IDA

MF

GO:0004677

DNA-dependent protein kinase activity

Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of DNA.

IDA

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:0008301

DNA binding, bending

The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.

IDA|IMP

MF

GO:0031492

nucleosomal DNA binding

Interacting selectively and non-covalently with the DNA portion of a nucleosome.

IDA

MF

GO:0035497

cAMP response element binding

Interacting 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.

IDA

MF

GO:0035500

MH2 domain binding

Interacting selectively and non-covalently with the MH2 (MAD homology 2) domain of a protein. The MH2 domain is found at the carboxy terminus of MAD related proteins such as Smads. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers.

IDA

MF

GO:0035501

MH1 domain binding

Interacting 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.

IDA

MF

GO:0046332

SMAD binding

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

IPI

MF

GO:0051575

5'-deoxyribose-5-phosphate lyase activity

Catalysis of the beta-elimination of the 5' deoxyribose-5-phosphate at an abasic site in DNA where a DNA-(apurinic or apyrimidinic site) lyase has already cleaved the C-O-P bond 3' to the apurinic or apyrimidinic site.

IDA

MF

GO:0070742

C2H2 zinc finger domain binding

Interacting selectively and non-covalently with a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion.

IMP