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|IGI|IMP|TAS

BP

GO:0001975

response to amphetamine

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 amphetamine stimulus. Amphetamines consist of a group of compounds related to alpha-methylphenethylamine.

IEA

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:0006338

chromatin remodeling

Dynamic 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.

IC

BP

GO:0006346

methylation-dependent chromatin silencing

Repression of transcription by methylation of DNA, leading to the formation of heterochromatin.

IGI

BP

GO:0006351

transcription, DNA-templated

The cellular synthesis of RNA on a template of DNA.

IEA

BP

GO:0006476

protein deacetylation

The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.

IDA

BP

GO:0007596

blood coagulation

The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.

TAS

BP

GO:0008284

positive regulation of cell proliferation

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

IMP

BP

GO:0008285

negative regulation of cell proliferation

Any process that stops, prevents or reduces the rate or extent of cell proliferation.

IEA

BP

GO:0009913

epidermal cell differentiation

The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis.

ISS

BP

GO:0010629

negative regulation of gene expression

Any process that decreases 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.

IMP

BP

GO:0010870

positive regulation of receptor biosynthetic process

Any process that increases the frequency or rate of receptor biosynthesis. Receptor biosynthesis is the collection of chemical reactions and pathways resulting in the formation of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

IMP

BP

GO:0016032

viral process

A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

IEA

BP

GO:0016575

histone deacetylation

The modification of histones by removal of acetyl groups.

IMP

BP

GO:0031000

response to caffeine

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 caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.

IEA

BP

GO:0032496

response to lipopolysaccharide

Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.

IEA

BP

GO:0032732

positive regulation of interleukin-1 production

Any process that activates or increases the frequency, rate, or extent of interleukin-1 production.

IEA

BP

GO:0032760

positive regulation of tumor necrosis factor production

Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.

IEA

BP

GO:0032922

circadian regulation of gene expression

Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.

ISS

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.

IEA

BP

GO:0042475

odontogenesis of dentin-containing tooth

The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel.

ISS

BP

GO:0042493

response to drug

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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.

IEA

BP

GO:0042517

positive regulation of tyrosine phosphorylation of Stat3 protein

Any process that activates or increases the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a Stat3 protein.

IEA

BP

GO:0042733

embryonic digit morphogenesis

The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.

ISS

BP

GO:0043044

ATP-dependent chromatin remodeling

Dynamic 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.

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.

ISS

BP

GO:0043524

negative regulation of neuron apoptotic process

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

IEA

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.

IMP

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.

IMP|ISS

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

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:0046676

negative regulation of insulin secretion

Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin.

IEA

BP

GO:0048714

positive regulation of oligodendrocyte differentiation

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

IEA

BP

GO:0055093

response to hyperoxia

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 indicating increased oxygen tension.

IEA

BP

GO:0060766

negative regulation of androgen receptor signaling pathway

Any process that decreases the rate, frequency, or extent of the androgen receptor signaling pathway.

IDA

BP

GO:0060789

hair follicle placode formation

The developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud.

ISS

BP

GO:0061029

eyelid development in camera-type eye

The progression of the eyelid in a camera-type eye from its formation to the mature state. The eyelid is a membranous cover that helps protect and lubricate the eye.

ISS

BP

GO:0061198

fungiform papilla formation

The developmental process pertaining to the initial formation of a spongiform papilla from unspecified parts. The fungiform papilla is a mushroom-shaped papilla of the tongue.

ISS

BP

GO:0070932

histone H3 deacetylation

The modification of histone H3 by the removal of one or more acetyl groups.

IDA

BP

GO:0070933

histone H4 deacetylation

The modification of histone H4 by the removal of one or more acetyl groups.

IDA

BP

GO:0071356

cellular response to tumor necrosis factor

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 tumor necrosis factor stimulus.

IEA

BP

GO:0090090

negative regulation of canonical Wnt signaling pathway

Any 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.

IGI

BP

GO:1901796

regulation of signal transduction by p53 class mediator

Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.

TAS

BP

GO:1904837

beta-catenin-TCF complex assembly

The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.

TAS

BP

GO:2000343

positive regulation of chemokine (C-X-C motif) ligand 2 production

Any process that activates or increases the frequency, rate or extent of chemokine (C-X-C motif) ligand 2 production.

IEA

BP

GO:2000676

positive regulation of type B pancreatic cell apoptotic process

Any process that activates or increases the frequency, rate or extent of type B pancreatic cell apoptotic process.

IEA

BP

GO:2000757

negative regulation of peptidyl-lysine acetylation

Any process that stops, prevents or reduces the frequency, rate or extent of peptidyl-lysine acetylation.

IEA

CC

GO:0000118

histone deacetylase complex

A protein complex that possesses histone deacetylase activity.

TAS

CC

GO:0000785

chromatin

The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.

IDA

CC

GO:0000790

nuclear chromatin

The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.

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:0005654

nucleoplasm

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

IDA|TAS

CC

GO:0005737

cytoplasm

All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

TAS

CC

GO:0005829

cytosol

The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

IDA

CC

GO:0016580

Sin3 complex

A 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.

IDA

CC

GO:0016581

NuRD complex

An 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.

IDA

CC

GO:0043005

neuron projection

A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.

IEA

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

CC

GO:0048471

perinuclear region of cytoplasm

Cytoplasm situated near, or occurring around, the nucleus.

IEA

MF

GO:0000976

transcription regulatory region sequence-specific DNA binding

Interacting 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.

ISS

MF

GO:0000978

RNA polymerase II core promoter proximal region sequence-specific DNA 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.

IDA

MF

GO:0000980

RNA polymerase II distal enhancer sequence-specific DNA binding

Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.

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:0001085

RNA polymerase II transcription factor binding

Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.

IPI

MF

GO:0001103

RNA polymerase II repressing transcription factor binding

Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription.

IPI

MF

GO:0001106

RNA polymerase II transcription corepressor activity

Interacting selectively and non-covalently with an RNA polymerase II repressing 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. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.

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.

TAS

MF

GO:0004407

histone deacetylase activity

Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.

IDA|IMP|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|TAS

MF

GO:0019213

deacetylase activity

Catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.

ISS

MF

GO:0019899

enzyme binding

Interacting selectively and non-covalently with any enzyme.

IPI

MF

GO:0031492

nucleosomal DNA binding

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

IDA

MF

GO:0032041

NAD-dependent histone deacetylase activity (H3-K14 specific)

Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein.

IEA

MF

GO:0033558

protein deacetylase activity

Catalysis of the hydrolysis of an acetyl group or groups from a protein substrate.

IDA|IMP

MF

GO:0033613

activating transcription factor binding

Interacting selectively and non-covalently with an activating transcription factor, any protein whose activity is required to initiate or upregulate transcription.

IPI

MF

GO:0042826

histone deacetylase binding

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

IPI

MF

GO:0044212

transcription regulatory region DNA binding

Interacting 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.

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.

IDA

MF

GO:0051059

NF-kappaB binding

Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.

IPI

MF

GO:0070491

repressing transcription factor binding

Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.

IPI