BP

GO:0000086

G2/M transition of mitotic cell cycle

The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.

TAS

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.

TAS

BP

GO:0000165

MAPK cascade

An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.

TAS

BP

GO:0000184

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.

TAS

BP

GO:0000187

activation of MAPK activity

The initiation of the activity of the inactive enzyme MAP kinase (MAPK).

TAS

BP

GO:0000209

protein polyubiquitination

Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.

TAS

BP

GO:0000715

nucleotide-excision repair, DNA damage recognition

The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix.

TAS

BP

GO:0000717

nucleotide-excision repair, DNA duplex unwinding

The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.

TAS

BP

GO:0002223

stimulatory C-type lectin receptor signaling pathway

Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.

TAS

BP

GO:0002755

MyD88-dependent toll-like receptor signaling pathway

Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.

TAS

BP

GO:0002756

MyD88-independent toll-like receptor signaling pathway

Any series of molecular signals generated as a consequence of binding to a toll-like receptor not relying on the MyD88 adaptor molecule. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.

TAS

BP

GO:0005978

glycogen biosynthetic process

The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.

TAS

BP

GO:0006283

transcription-coupled nucleotide-excision repair

The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.

TAS

BP

GO:0006294

nucleotide-excision repair, preincision complex assembly

The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.

TAS

BP

GO:0006296

nucleotide-excision repair, DNA incision, 5'-to lesion

The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.

TAS

BP

GO:0006297

nucleotide-excision repair, DNA gap filling

Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.

TAS

BP

GO:0006364

rRNA processing

Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.

TAS

BP

GO:0006412

translation

The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome.

IC

BP

GO:0006413

translational initiation

The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA.

TAS

BP

GO:0006614

SRP-dependent cotranslational protein targeting to membrane

The targeting of proteins to a membrane that occurs during translation and is dependent upon two key components, the signal-recognition particle (SRP) and the SRP receptor. SRP is a cytosolic particle that transiently binds to the endoplasmic reticulum (ER) signal sequence in a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.

TAS

BP

GO:0006977

DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest

A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.

TAS

BP

GO:0007179

transforming growth factor beta receptor signaling pathway

A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.

TAS

BP

GO:0007219

Notch signaling pathway

A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.

TAS

BP

GO:0007249

I-kappaB kinase/NF-kappaB signaling

The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.

TAS

BP

GO:0007254

JNK cascade

An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.

TAS

BP

GO:0008543

fibroblast growth factor receptor signaling pathway

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

TAS

BP

GO:0010803

regulation of tumor necrosis factor-mediated signaling pathway

Any process that modulates the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.

TAS

BP

GO:0010939

regulation of necrotic cell death

Any process that modulates the rate, frequency or extent of necrotic cell death. Necrotic cell death is a cell death process that is morphologically characterized by a gain in cell volume (oncosis), swelling of organelles, plasma membrane rupture and subsequent loss of intracellular contents.

TAS

BP

GO:0016055

Wnt signaling pathway

The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.

TAS

BP

GO:0016197

endosomal transport

The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.

TAS

BP

GO:0016236

macroautophagy

The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.

TAS

BP

GO:0019058

viral life cycle

A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.

TAS

BP

GO:0019068

virion assembly

A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.

TAS

BP

GO:0019083

viral transcription

The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.

TAS

BP

GO:0019985

translesion synthesis

The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.

TAS

BP

GO:0030512

negative regulation of transforming growth factor beta receptor signaling pathway

Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.

TAS

BP

GO:0031145

anaphase-promoting complex-dependent 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, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.

TAS

BP

GO:0032479

regulation of type I interferon production

Any process that modulates the frequency, rate, or extent of interferon type I production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.

TAS

BP

GO:0032480

negative regulation of type I interferon production

Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.

TAS

BP

GO:0033209

tumor necrosis factor-mediated signaling pathway

A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.

TAS

BP

GO:0033683

nucleotide-excision repair, DNA incision

A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.

TAS

BP

GO:0034220

ion transmembrane transport

A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.

TAS

BP

GO:0035666

TRIF-dependent toll-like receptor signaling pathway

Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.

TAS

BP

GO:0036297

interstrand cross-link repair

Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA. DNA interstrand crosslinks occur when both strands of duplex DNA are covalently tethered together (e.g. by an exogenous or endogenous agent), thus preventing the strand unwinding necessary for essential DNA functions such as transcription and replication.

TAS

BP

GO:0038061

NIK/NF-kappaB signaling

The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).

TAS

BP

GO:0038095

Fc-epsilon receptor signaling pathway

A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.

TAS

BP

GO:0038128

ERBB2 signaling pathway

A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.

TAS

BP

GO:0042059

negative regulation of epidermal growth factor receptor signaling pathway

Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.

TAS

BP

GO:0042276

error-prone translesion synthesis

The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.

TAS

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.

TAS

BP

GO:0042787

protein ubiquitination involved in ubiquitin-dependent protein catabolic process

The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.

TAS

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.

TAS

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.

TAS

BP

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.

TAS

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.

TAS

BP

GO:0043488

regulation of mRNA stability

Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.

TAS

BP

GO:0044267

cellular protein metabolic process

The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.

TAS

BP

GO:0045087

innate immune response

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

TAS

BP

GO:0045742

positive regulation of epidermal growth factor receptor signaling pathway

Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.

TAS

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.

TAS

BP

GO:0050852

T cell receptor signaling pathway

A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.

TAS

BP

GO:0051092

positive regulation of NF-kappaB transcription factor activity

Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.

TAS

BP

GO:0051403

stress-activated MAPK cascade

A series of molecular signals in which a stress-activated MAP kinase cascade relays one or more of the signals; MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase.

TAS

BP

GO:0051436

negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle

Any process that stops, prevents, or reduces the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.

TAS

BP

GO:0051437

positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition

Any process that activates, maintains or increases the rate of ubiquitin ligase activity that contributes to the regulation of the mitotic cell cycle phase transition.

TAS

BP

GO:0060071

Wnt signaling pathway, planar cell polarity pathway

The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity.

TAS

BP

GO:0061418

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

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

TAS

BP

GO:0070423

nucleotide-binding oligomerization domain containing signaling pathway

Any series of molecular signals generated as a consequence of binding to a nucleotide-binding oligomerization domain containing (NOD) protein.

TAS

BP

GO:0070911

global genome nucleotide-excision repair

The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.

TAS

BP

GO:0070987

error-free translesion synthesis

The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.

TAS

BP

GO:0075733

intracellular transport of virus

The directed movement of a virus, or part of a virus, within the host cell.

TAS

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.

TAS

BP

GO:0090263

positive regulation of canonical Wnt signaling pathway

Any process that increases 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.

TAS

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

CC

GO:0005615

extracellular space

That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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.

TAS

CC

GO:0005730

nucleolus

A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.

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.

TAS

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.

TAS

CC

GO:0010008

endosome membrane

The lipid bilayer surrounding an endosome.

TAS

CC

GO:0015935

small ribosomal subunit

The smaller of the two subunits of a ribosome.

IDA

CC

GO:0016020

membrane

A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

IDA

CC

GO:0022627

cytosolic small ribosomal subunit

The small subunit of a ribosome located in the cytosol.

IDA

CC

GO:0030666

endocytic vesicle membrane

The lipid bilayer surrounding an endocytic vesicle.

TAS

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.

IEA

CC

GO:0070062

extracellular exosome

A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

IDA

MF

GO:0003735

structural constituent of ribosome

The action of a molecule that contributes to the structural integrity of the ribosome.

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: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:0046872

metal ion binding

Interacting selectively and non-covalently with any metal ion.

IEA