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

BP

GO:0001501

skeletal system development

The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).

IEA

BP

GO:0002076

osteoblast development

The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone.

IEA

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.

IDA

BP

GO:0006351

transcription, DNA-templated

The cellular synthesis of RNA on a template of DNA.

IEA

BP

GO:0006954

inflammatory response

The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.

TAS

BP

GO:0007399

nervous system development

The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.

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:0010592

positive regulation of lamellipodium assembly

Any process that increases the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.

IEA

BP

GO:0010832

negative regulation of myotube differentiation

Any process that decreases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.

IMP

BP

GO:0010882

regulation of cardiac muscle contraction by calcium ion signaling

Any process that modulates the frequency, rate or extent of cardiac muscle contraction by changing the calcium ion signals that trigger contraction.

IEA

BP

GO:0014894

response to denervation involved in regulation of muscle adaptation

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 denervation stimulus. This process occurs as part of the regulation of muscle adaptation.

ISS

BP

GO:0014898

cardiac muscle hypertrophy in response to stress

The physiological enlargement or overgrowth of all or part of the heart muscle due to an increase in size (not length) of individual cardiac muscle fibers, without cell division, as a result of a disturbance in organismal or cellular homeostasis.

TAS

BP

GO:0014911

positive regulation of smooth muscle cell migration

Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.

IEA

BP

GO:0016575

histone deacetylation

The modification of histones by removal of acetyl groups.

IDA|IMP

BP

GO:0030183

B cell differentiation

The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.

TAS

BP

GO:0033235

positive regulation of protein sumoylation

Any process that activates or increases the frequency, rate or extent of the addition of SUMO groups to a protein.

IDA

BP

GO:0034983

peptidyl-lysine deacetylation

The removal of an acetyl group from an acetylated lysine residue in a peptide or protein.

IDA

BP

GO:0040029

regulation of gene expression, epigenetic

Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.

IMP

BP

GO:0042113

B cell activation

The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.

TAS

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:0043393

regulation of protein binding

Any process that modulates the frequency, rate or extent of protein binding.

IMP

BP

GO:0043433

negative regulation of sequence-specific DNA binding transcription factor activity

Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.

IMP

BP

GO:0043525

positive regulation of neuron apoptotic process

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

IEA

BP

GO:0045668

negative regulation of osteoblast differentiation

Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.

IEA

BP

GO:0045820

negative regulation of glycolytic process

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

ISS

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.

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.

IMP|ISS

BP

GO:0048661

positive regulation of smooth muscle cell proliferation

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

IEA

BP

GO:0048742

regulation of skeletal muscle fiber development

Any process that modulates the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.

IEA

BP

GO:0051091

positive regulation of sequence-specific DNA binding transcription factor activity

Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.

IMP

BP

GO:0070555

response to interleukin-1

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 interleukin-1 stimulus.

IMP

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:0071260

cellular response to mechanical 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 mechanical stimulus.

IEA

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:0071374

cellular response to parathyroid hormone 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 parathyroid hormone stimulus.

IEA

BP

GO:1903428

positive regulation of reactive oxygen species biosynthetic process

Any process that activates or increases the frequency, rate or extent of reactive oxygen species biosynthetic process.

IEA

CC

GO:0000118

histone deacetylase complex

A protein complex that possesses histone deacetylase activity.

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

CC

GO:0005737

cytoplasm

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

IDA

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.

IEA

CC

GO:0017053

transcriptional repressor complex

A protein complex that possesses activity that prevents or downregulates transcription.

IDA

CC

GO:0030018

Z disc

Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.

IEA

CC

GO:0031594

neuromuscular junction

The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.

IEA

CC

GO:0031672

A band

The dark-staining region of a sarcomere, in which myosin thick filaments are present; the center is traversed by the paler H zone, which in turn contains the M line.

IEA

CC

GO:0042641

actomyosin

Any complex of actin, myosin, and accessory proteins.

IEA

MF

GO:0001025

RNA polymerase III transcription factor binding

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

IPI

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: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.

IEA

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.

IEA

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

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.

IDA

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.

IEA

MF

GO:0030955

potassium ion binding

Interacting selectively and non-covalently with potassium (K+) ions.

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

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: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.

IDA

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: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