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:0000186

activation of MAPKK activity

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

IEA

BP

GO:0002250

adaptive immune response

An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).

IEA

BP

GO:0006468

protein phosphorylation

The process of introducing a phosphate group on to a protein.

TAS

BP

GO:0006915

apoptotic process

A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.

ISS

BP

GO:0006919

activation of cysteine-type endopeptidase activity involved in apoptotic process

Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.

ISS

BP

GO:0006928

movement of cell or subcellular component

The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.

TAS

BP

GO:0007165

signal transduction

The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.

ISS

BP

GO:0007167

enzyme linked receptor protein signaling pathway

Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription.

ISS

BP

GO:0007186

G-protein coupled receptor signaling pathway

A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).

IEA

BP

GO:0007204

positive regulation of cytosolic calcium ion concentration

Any process that increases the concentration of calcium ions in the cytosol.

IEA

BP

GO:0007259

JAK-STAT cascade

Any process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The JAK-STAT cascade begins with activation of STAT proteins by members of the JAK family of tyrosine kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins.

TAS

BP

GO:0007260

tyrosine phosphorylation of STAT protein

The process of introducing a phosphate group to a tyrosine residue of a STAT (Signal Transducer and Activator of Transcription) protein.

IBA|ISS

BP

GO:0007262

STAT protein import into nucleus

The directed movement of dimerized STAT (Signal Transducers and Activators of Transcription) proteins into the nucleus following activation by members of the janus activated kinase (JAK) family of tyrosine kinases.

ISS

BP

GO:0007498

mesoderm development

The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.

TAS

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:0008285

negative regulation of cell proliferation

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

ISS

BP

GO:0008631

intrinsic apoptotic signaling pathway in response to oxidative stress

A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, and ends when the execution phase of apoptosis is triggered.

IEA

BP

GO:0010667

negative regulation of cardiac muscle cell apoptotic process

Any process that decreases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.

IEA

BP

GO:0010811

positive regulation of cell-substrate adhesion

Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.

IDA

BP

GO:0014068

positive regulation of phosphatidylinositol 3-kinase signaling

Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.

ISS

BP

GO:0016477

cell migration

The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.

IBA

BP

GO:0018108

peptidyl-tyrosine phosphorylation

The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.

ISS

BP

GO:0019221

cytokine-mediated signaling pathway

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

IDA|ISS

BP

GO:0022408

negative regulation of cell-cell adhesion

Any process that stops, prevents or reduces the rate or extent of cell adhesion to another cell.

IEA

BP

GO:0030041

actin filament polymerization

Assembly of actin filaments by the addition of actin monomers to a filament.

NAS

BP

GO:0030154

cell differentiation

The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.

ISS

BP

GO:0030218

erythrocyte differentiation

The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.

IBA|ISS

BP

GO:0030335

positive regulation of cell migration

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

IEA

BP

GO:0031103

axon regeneration

The regrowth of axons following their loss or damage.

IEA

BP

GO:0031959

mineralocorticoid receptor signaling pathway

Any series of molecular signals generated as a consequence of a mineralocorticoid binding to its receptor.

IEA

BP

GO:0032024

positive regulation of insulin secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of insulin.

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.

ISS

BP

GO:0032516

positive regulation of phosphoprotein phosphatase activity

Any process that activates or increases the activity of a phosphoprotein phosphatase.

IEA

BP

GO:0032731

positive regulation of interleukin-1 beta production

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

ISS

BP

GO:0033160

positive regulation of protein import into nucleus, translocation

Any process that activates or increases the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.

IEA

BP

GO:0033194

response to hydroperoxide

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 hydroperoxide stimulus. Hydroperoxides are monosubstitution products of hydrogen peroxide, HOOH.

IEA

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.

IDA

BP

GO:0034612

response to tumor necrosis factor

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 tumor necrosis factor stimulus.

IDA

BP

GO:0035409

histone H3-Y41 phosphorylation

The modification of histone H3 by the addition of a phosphate group to a tyrosine residue at position 41 of the histone.

IDA

BP

GO:0035556

intracellular signal transduction

The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.

ISS

BP

GO:0035722

interleukin-12-mediated signaling pathway

A series of molecular signals initiated by the binding of interleukin-12 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.

IDA

BP

GO:0038083

peptidyl-tyrosine autophosphorylation

The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.

IBA

BP

GO:0042127

regulation of cell proliferation

Any process that modulates the frequency, rate or extent of cell proliferation.

IBA

BP

GO:0042503

tyrosine phosphorylation of Stat3 protein

The process of introducing a phosphate group to a tyrosine residue of a Stat3 protein.

IEA

BP

GO:0042506

tyrosine phosphorylation of Stat5 protein

The process of introducing a phosphate group to a tyrosine residue of a Stat5 protein.

IEA

BP

GO:0042508

tyrosine phosphorylation of Stat1 protein

The process of introducing a phosphate group to a tyrosine residue of a Stat1 protein.

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.

ISS

BP

GO:0042523

positive regulation of tyrosine phosphorylation of Stat5 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 Stat5 protein.

ISS

BP

GO:0042977

activation of JAK2 kinase activity

The process of introducing a phosphate group to a tyrosine residue of a JAK2 (Janus Activated Kinase 2) protein, thereby activating it.

ISS

BP

GO:0042981

regulation of apoptotic process

Any process that modulates the occurrence or rate of cell death by apoptotic process.

IBA

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:0043392

negative regulation of DNA binding

Any process that stops or reduces 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: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:0043547

positive regulation of GTPase activity

Any process that activates or increases the activity of a GTPase.

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.

IBA

BP

GO:0045429

positive regulation of nitric oxide biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.

IEA

BP

GO:0045597

positive regulation of cell differentiation

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

IEA

BP

GO:0045822

negative regulation of heart contraction

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

IEA

BP

GO:0046677

response to antibiotic

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 antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

IDA

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).

ISS

BP

GO:0048008

platelet-derived growth factor receptor signaling pathway

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

IEA

BP

GO:0050727

regulation of inflammatory response

Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.

IDA

BP

GO:0050729

positive regulation of inflammatory response

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

IEA

BP

GO:0050731

positive regulation of peptidyl-tyrosine phosphorylation

Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.

ISS

BP

GO:0050867

positive regulation of cell activation

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

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.

IEA

BP

GO:0051770

positive regulation of nitric-oxide synthase biosynthetic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme.

ISS

BP

GO:0060333

interferon-gamma-mediated signaling pathway

A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.

TAS

BP

GO:0060334

regulation of interferon-gamma-mediated signaling pathway

Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor.

TAS

BP

GO:0060396

growth hormone receptor signaling pathway

The series of molecular signals generated as a consequence of growth hormone receptor binding to its physiological ligand.

IDA

BP

GO:0060397

JAK-STAT cascade involved in growth hormone signaling pathway

The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.

ISS|TAS

BP

GO:0060399

positive regulation of growth hormone receptor signaling pathway

Any process that increases the rate, frequency or extent of the growth hormone receptor signaling pathway. The growth hormone receptor signaling pathway is the series of molecular signals generated as a consequence of growth hormone receptor binding to its physiological ligand.

ISS

BP

GO:0061180

mammary gland epithelium development

The process whose specific outcome is the progression of the mammary gland epithelium over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.

ISS

BP

GO:0070671

response to interleukin-12

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-12 stimulus.

IDA

BP

GO:0097191

extrinsic apoptotic signaling pathway

A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered.

ISS

BP

GO:0097296

activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway

Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the apoptotic signaling pathway.

ISS

BP

GO:1902728

positive regulation of growth factor dependent skeletal muscle satellite cell proliferation

Any process that activates or increases the frequency, rate or extent of satellite cell proliferation; dependent on specific growth factor activity such as fibroblast growth factors and transforming growth factor beta.

IEA

BP

GO:1904037

positive regulation of epithelial cell apoptotic process

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

IEA

BP

GO:1904707

positive regulation of vascular smooth muscle cell proliferation

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

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:0005654

nucleoplasm

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

TAS

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:0005856

cytoskeleton

Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

IEA

CC

GO:0005901

caveola

A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.

ISS

CC

GO:0016363

nuclear matrix

The dense fibrillar network lying on the inner side of the nuclear membrane.

IEA

CC

GO:0031234

extrinsic component of cytoplasmic side of plasma membrane

The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.

IBA

CC

GO:0031904

endosome lumen

The volume enclosed by the membrane of an endosome.

TAS

CC

GO:0045121

membrane raft

Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.

ISS

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.

NAS

MF

GO:0004713

protein tyrosine kinase activity

Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.

EXP|IDA|ISS|TAS

MF

GO:0004715

non-membrane spanning protein tyrosine kinase activity

Catalysis of the reaction: ATP + a non-membrane spanning protein L-tyrosine = ADP + a non-membrane spanning protein L-tyrosine phosphate.

IBA|TAS

MF

GO:0005088

Ras guanyl-nucleotide exchange factor activity

Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.

TAS

MF

GO:0005102

receptor binding

Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

IPI

MF

GO:0005131

growth hormone receptor binding

Interacting selectively and non-covalently with the growth hormone receptor.

IBA|ISS

MF

GO:0005143

interleukin-12 receptor binding

Interacting selectively and non-covalently with the interleukin-12 receptor.

ISS

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:0005524

ATP binding

Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

IEA

MF

GO:0008022

protein C-terminus binding

Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.

IEA

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.

IDA

MF

GO:0020037

heme binding

Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.

IDA

MF

GO:0031702

type 1 angiotensin receptor binding

Interacting selectively and non-covalently with a type 1 angiotensin receptor.

IEA

MF

GO:0033130

acetylcholine receptor binding

Interacting selectively and non-covalently with an acetylcholine receptor.

IEA

MF

GO:0035401

histone kinase activity (H3-Y41 specific)

The modification of histone H3 by the addition of a phosphate group to a tyrosine residue at position 41 of the histone.

IDA

MF

GO:0042169

SH2 domain binding

Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.

IPI

MF

GO:0042393

histone binding

Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.

IDA

MF

GO:0043548

phosphatidylinositol 3-kinase binding

Interacting selectively and non-covalently with a phosphatidylinositol 3-kinase, any enzyme that catalyzes the addition of a phosphate group to an inositol lipid at the 3' position of the inositol ring.

IEA

MF

GO:0043560

insulin receptor substrate binding

Interacting selectively and non-covalently with any of the insulin receptor substrate (IRS) proteins, adaptor proteins that bind to the transphosphorylated insulin and insulin-like growth factor receptors, are themselves phosphorylated and in turn recruit SH2 domain-containing signaling molecules to form a productive signaling complex.

IEA

MF

GO:0046872

metal ion binding

Interacting selectively and non-covalently with any metal ion.

IEA

MF

GO:0051428

peptide hormone receptor binding

Interacting selectively and non-covalently with a receptor for peptide hormones.

IEA