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.

IEA

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.

ISS

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.

IDA

BP

GO:0006367

transcription initiation from RNA polymerase II promoter

Any 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.

TAS

BP

GO:0007265

Ras protein signal transduction

A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.

IMP

BP

GO:0007566

embryo implantation

Attachment of the blastocyst to the uterine lining.

IEA

BP

GO:0016567

protein ubiquitination

The process in which one or more ubiquitin groups are added to a protein.

IEA

BP

GO:0016569

chromatin modification

The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups.

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.

IDA|IEA

BP

GO:0042993

positive regulation of transcription factor import into nucleus

Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.

IDA

BP

GO:0043045

DNA methylation involved in embryo development

The covalent transfer of a methyl group to C-5 of cytosine that contributes to the epigenetic regulation of embryonic gene expression.

IEA

BP

GO:0043388

positive regulation of DNA binding

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

IEA

BP

GO:0045087

innate immune response

Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.

IDA

BP

GO:0045739

positive regulation of DNA repair

Any process that activates or increases the frequency, rate or extent of DNA repair.

IDA

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.

IEA

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

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.

ISS

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:0046777

protein autophosphorylation

The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).

IEA

BP

GO:0051259

protein oligomerization

The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.

IDA

BP

GO:0060028

convergent extension involved in axis elongation

The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis contributing to the lengthening of the axis of an organism.

IEA

BP

GO:0060669

embryonic placenta morphogenesis

The process in which the embryonic placenta is generated and organized.

IEA

BP

GO:0090309

positive regulation of methylation-dependent chromatin silencing

Any process that increases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.

IMP

BP

GO:1901536

negative regulation of DNA demethylation

Any process that stops, prevents or reduces the frequency, rate or extent of DNA demethylation.

IEA

BP

GO:1902187

negative regulation of viral release from host cell

Any process that stops, prevents or reduces the frequency, rate or extent of viral release from host cell.

IDA

BP

GO:2000653

regulation of genetic imprinting

Any process that modulates the frequency, rate or extent of genetic imprinting.

IEA

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|ISS

CC

GO:0005654

nucleoplasm

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

IDA|TAS

CC

GO:0005719

nuclear euchromatin

The 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.

IEA

CC

GO:0005720

nuclear heterochromatin

A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.

IEA

CC

GO:0090575

RNA polymerase II transcription factor complex

A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.

ISS

MF

GO:0001105

RNA polymerase II transcription coactivator activity

Interacting 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 extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.

ISS

MF

GO:0003677

DNA binding

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

IDA

MF

GO:0003682

chromatin binding

Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.

IDA

MF

GO:0003700

transcription factor activity, sequence-specific DNA binding

Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.

ISS

MF

GO:0003714

transcription corepressor activity

Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.

IDA

MF

GO:0004672

protein kinase activity

Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.

IEA

MF

GO:0004842

ubiquitin-protein transferase activity

Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.

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:0008270

zinc ion binding

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

IDA

MF

GO:0016874

ligase activity

Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.

IEA

MF

GO:0031625

ubiquitin protein ligase binding

Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.

IDA

MF

GO:0035851

Krueppel-associated box domain binding

Interacting 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.

IDA

MF

GO:0043565

sequence-specific DNA binding

Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.

ISS

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:0070087

chromo shadow domain binding

Interacting selectively and non-covalently with a chromo shadow domain, a protein domain that is distantly related, and found in association with, the chromo domain.

IPI

MF

GO:1990841

promoter-specific chromatin binding

Interacting selectively and non-covalently with a section of chromatin that is associated with gene promoter sequences of DNA.

IDA