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|IMP

BP

GO:0000183

chromatin silencing at rDNA

Repression of transcription of ribosomal DNA by altering the structure of chromatin.

NAS

BP

GO:0006342

chromatin silencing

Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.

NAS

BP

GO:0006348

chromatin silencing at telomere

Repression of transcription of telomeric DNA by altering the structure of chromatin.

NAS

BP

GO:0006351

transcription, DNA-templated

The cellular synthesis of RNA on a template of DNA.

IEA

BP

GO:0006471

protein ADP-ribosylation

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

NAS

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|IMP

BP

GO:0006914

autophagy

The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.

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:0007096

regulation of exit from mitosis

Any process involved in the progression from anaphase/telophase to G1 that is associated with a conversion from high to low mitotic CDK activity.

NAS

BP

GO:0008285

negative regulation of cell proliferation

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

IMP

BP

GO:0010507

negative regulation of autophagy

Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.

IMP

BP

GO:0010801

negative regulation of peptidyl-threonine phosphorylation

Any process that decreases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.

ISS

BP

GO:0014065

phosphatidylinositol 3-kinase signaling

A series of reactions within the signal-receiving cell, mediated by the intracellular phosphatidylinositol 3-kinase (PI3K). Many cell surface receptor linked signaling pathways signal through PI3K to regulate numerous cellular functions.

IMP

BP

GO:0016458

gene silencing

Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression.

NAS

BP

GO:0016575

histone deacetylation

The modification of histones by removal of acetyl groups.

TAS

BP

GO:0021762

substantia nigra development

The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).

IEP

BP

GO:0022011

myelination in peripheral nervous system

The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of Schwann cells in the peripheral nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.

ISS

BP

GO:0031641

regulation of myelination

Any process that modulates the frequency, rate or extent of the formation of a myelin sheath around nerve axons.

ISS

BP

GO:0032436

positive regulation of proteasomal ubiquitin-dependent protein catabolic process

Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.

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.

ISS

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:0035729

cellular response to hepatocyte growth factor 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 hepatocyte growth factor stimulus.

IDA

BP

GO:0042177

negative regulation of protein catabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.

IMP

BP

GO:0042325

regulation of phosphorylation

Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.

NAS

BP

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.

IMP

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).

ISS

BP

GO:0043491

protein kinase B signaling

A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound.

IMP

BP

GO:0044242

cellular lipid catabolic process

The chemical reactions and pathways resulting in the breakdown of lipids, as carried out by individual cells.

ISS

BP

GO:0045087

innate immune response

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

IEA

BP

GO:0045599

negative regulation of fat cell differentiation

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

ISS

BP

GO:0045836

positive regulation of meiotic nuclear division

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

ISS

BP

GO:0045843

negative regulation of striated muscle tissue development

Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle development.

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

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|ISS

BP

GO:0048012

hepatocyte growth factor receptor signaling pathway

The series of molecular signals generated as a consequence of the hepatocyte growth factor receptor binding to one of its physiological ligands.

IDA

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:0051321

meiotic cell cycle

Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.

IEA

BP

GO:0051726

regulation of cell cycle

Any process that modulates the rate or extent of progression through the cell cycle.

IMP

BP

GO:0051775

response to redox state

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 redox state. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.

NAS

BP

GO:0051781

positive regulation of cell division

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

ISS

BP

GO:0051987

positive regulation of attachment of spindle microtubules to kinetochore

Any process that activates or increases the frequency, rate or extent of the attachment of spindle microtubules to the kinetochore.

ISS

BP

GO:0061428

negative regulation of transcription from RNA polymerase II promoter in response to hypoxia

Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.

IMP

BP

GO:0061433

cellular response to caloric restriction

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 of caloric restriction, insufficient food energy intake.

ISS

BP

GO:0070446

negative regulation of oligodendrocyte progenitor proliferation

Any process that stops or decreases the rate or extent of oligodendrocyte progenitor proliferation.

ISS

BP

GO:0070932

histone H3 deacetylation

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

IMP

BP

GO:0070933

histone H4 deacetylation

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

IDA

BP

GO:0071219

cellular response to molecule of bacterial origin

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 by molecules of bacterial origin such as peptides derived from bacterial flagellin.

IDA

BP

GO:0071456

cellular response to hypoxia

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 lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.

IDA

BP

GO:0071872

cellular response to epinephrine 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 epinephrine stimulus. Epinephrine is a catecholamine that has the formula C9H13NO3; it is secreted by the adrenal medulla to act as a hormone, and released by certain neurons to act as a neurotransmitter active in the central nervous system.

ISS

BP

GO:0090042

tubulin deacetylation

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

IDA|IMP|ISS

BP

GO:1900119

positive regulation of execution phase of apoptosis

Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis.

ISS

BP

GO:1900195

positive regulation of oocyte maturation

Any process that activates or increases the frequency, rate or extent of oocyte maturation.

ISS

BP

GO:1900226

negative regulation of NLRP3 inflammasome complex assembly

Any process that stops, prevents or reduces the frequency, rate or extent of NLRP3 inflammasome complex assembly.

IEA

BP

GO:1900425

negative regulation of defense response to bacterium

Any process that stops, prevents or reduces the frequency, rate or extent of defense response to bacterium.

IMP

BP

GO:1901026

ripoptosome assembly involved in necroptotic process

The aggregation, arrangement and bonding together of ripoptosome components leading to a necroptotic process.

IEA

BP

GO:2000378

negative regulation of reactive oxygen species metabolic process

Any process that stops, prevents or reduces the frequency, rate or extent of reactive oxygen species metabolic process.

ISS

BP

GO:2000777

positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia

Any positive regulation of proteasomal ubiquitin-dependent protein catabolic process that is involved in a cellular response to hypoxia.

IMP

CC

GO:0000781

chromosome, telomeric region

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

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

CC

GO:0005677

chromatin silencing complex

Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing.

NAS

CC

GO:0005694

chromosome

A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.

IDA

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.

ISS

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:0005813

centrosome

A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.

IDA

CC

GO:0005814

centriole

A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.

IDA

CC

GO:0005819

spindle

The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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.

IDA

CC

GO:0005874

microtubule

Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.

IDA

CC

GO:0005886

plasma membrane

The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

IEA

CC

GO:0030426

growth cone

The migrating motile tip of a growing nerve cell axon or dendrite.

IEA

CC

GO:0030496

midbody

A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.

IDA

CC

GO:0033010

paranodal junction

A highly specialized cell-cell junction found in vertebrates, which forms between a neuron and a glial cell, and has structural similarity to Drosophila septate junctions. It flanks the node of Ranvier in myelinated nerve and electrically isolates the myelinated from unmyelinated nerve segments and physically separates the voltage-gated sodium channels at the node from the cluster of potassium channels underneath the myelin sheath.

ISS

CC

GO:0033270

paranode region of axon

An axon part that is located adjacent to the nodes of Ranvier and surrounded by lateral loop portions of myelin sheath.

ISS

CC

GO:0043204

perikaryon

The portion of the cell soma (cell body) that excludes the nucleus.

ISS

CC

GO:0043209

myelin sheath

An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.

ISS

CC

GO:0043219

lateral loop

Non-compact myelin located adjacent to the nodes of Ranvier in a myelin segment. These non-compact regions include cytoplasm from the cell responsible for synthesizing the myelin. Lateral loops are found in the paranodal region adjacent to the nodes of Ranvier, while Schmidt-Lantermann clefts are analogous structures found within the compact myelin internode.

ISS

CC

GO:0043220

Schmidt-Lanterman incisure

Regions within compact myelin in which the cytoplasmic faces of the enveloping myelin sheath are not tightly juxtaposed, and include cytoplasm from the cell responsible for making the myelin. Schmidt-Lanterman incisures occur in the compact myelin internode, while lateral loops are analogous structures found in the paranodal region adjacent to the nodes of Ranvier.

ISS

CC

GO:0044224

juxtaparanode region of axon

A region of an axon near a node of Ranvier that is between the paranode and internode regions.

ISS

CC

GO:0048471

perinuclear region of cytoplasm

Cytoplasm situated near, or occurring around, the nucleus.

ISS

CC

GO:0072686

mitotic spindle

A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.

IDA

CC

GO:0072687

meiotic spindle

A spindle that forms as part of meiosis. Several proteins, such as budding yeast Spo21p, fission yeast Spo2 and Spo13, and C. elegans mei-1, localize specifically to the meiotic spindle and are absent from the mitotic spindle.

ISS

CC

GO:0097386

glial cell projection

A prolongation or process extending from a glial cell.

ISS

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: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:0017136

NAD-dependent histone deacetylase activity

Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone.

IDA

MF

GO:0033558

protein deacetylase activity

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

IDA|IMP

MF

GO:0034979

NAD-dependent protein deacetylase activity

Catalysis of the removal of one or more acetyl groups from a protein, requiring NAD.

IDA|IMP

MF

GO:0035035

histone acetyltransferase binding

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

IPI

MF

GO:0042826

histone deacetylase binding

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

IPI

MF

GO:0042903

tubulin deacetylase activity

Catalysis of the reaction: N-acetyl(alpha-tubulin) + H2O = alpha-tubulin + acetate.

IDA

MF

GO:0043130

ubiquitin binding

Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.

IDA

MF

GO:0046970

NAD-dependent histone deacetylase activity (H4-K16 specific)

Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein.

IDA

MF

GO:0048487

beta-tubulin binding

Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin.

IEA

MF

GO:0070403

NAD+ binding

Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.

IDA