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:0000187

activation of MAPK activity

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

TAS

BP

GO:0000189

MAPK import into nucleus

The directed movement of a MAP kinase to the nucleus upon activation.

IEA

BP

GO:0006351

transcription, DNA-templated

The cellular synthesis of RNA on a template of DNA.

IEA

BP

GO:0006468

protein phosphorylation

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

IDA

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.

IEA

BP

GO:0006935

chemotaxis

The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).

TAS

BP

GO:0006950

response to stress

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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

TAS

BP

GO:0006974

cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

IEA

BP

GO:0007049

cell cycle

The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.

IEA

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.

TAS

BP

GO:0007268

chemical synaptic transmission

The vesicular release of classical neurotransmitter molecules from a neuron, across a chemical synapse, the subsequent activation of neurotransmitter receptors of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.

TAS

BP

GO:0007411

axon guidance

The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.

TAS

BP

GO:0008284

positive regulation of cell proliferation

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

IEA

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:0009636

response to toxic substance

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 toxic stimulus.

IEA

BP

GO:0010800

positive regulation of peptidyl-threonine phosphorylation

Any process that increases 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.

IDA

BP

GO:0014066

regulation of phosphatidylinositol 3-kinase signaling

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

TAS

BP

GO:0016032

viral process

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

IEA

BP

GO:0018105

peptidyl-serine phosphorylation

The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.

IDA

BP

GO:0018107

peptidyl-threonine phosphorylation

The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.

ISS

BP

GO:0019233

sensory perception of pain

The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.

IEA

BP

GO:0019858

cytosine metabolic process

The chemical reactions and pathways involving cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives.

IEA

BP

GO:0030168

platelet activation

A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.

TAS

BP

GO:0030278

regulation of ossification

Any process that modulates the frequency, rate or extent of bone formation.

IEA

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:0030878

thyroid gland development

The process whose specific outcome is the progression of the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone.

IEA

BP

GO:0031647

regulation of protein stability

Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.

ISS

BP

GO:0031663

lipopolysaccharide-mediated signaling pathway

A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.

IEA

BP

GO:0032212

positive regulation of telomere maintenance via telomerase

Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.

IMP

BP

GO:0032872

regulation of stress-activated MAPK cascade

Any process that modulates the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.

TAS

BP

GO:0033598

mammary gland epithelial cell proliferation

The multiplication or reproduction of mammary gland epithelial cells, resulting in the expansion of a cell population. Mammary gland epithelial cells make up the covering of surfaces of the mammary gland. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.

IEA

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:0038096

Fc-gamma receptor signaling pathway involved in phagocytosis

An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.

TAS

BP

GO:0038127

ERBB signaling pathway

A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptor tyrosine kinases on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.

IDA

BP

GO:0042473

outer ear morphogenesis

The process in which the anatomical structures of the outer ear are generated and organized. The outer ear is the part of the ear external to the tympanum (eardrum). It consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull.

IEA

BP

GO:0043330

response to exogenous dsRNA

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 exogenous double-stranded RNA stimulus.

IEA

BP

GO:0043627

response to estrogen

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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.

IEA

BP

GO:0045596

negative regulation of cell differentiation

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

IEA

BP

GO:0045727

positive regulation of translation

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.

IEA

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.

IEA

BP

GO:0048538

thymus development

The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.

IEA

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.

IEA

BP

GO:0050853

B cell receptor signaling pathway

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

IEA

BP

GO:0051090

regulation of sequence-specific DNA binding transcription factor activity

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

TAS

BP

GO:0051493

regulation of cytoskeleton organization

Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.

TAS

BP

GO:0051973

positive regulation of telomerase activity

Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

IMP

BP

GO:0060020

Bergmann glial cell differentiation

The process in which neuroepithelial cells of the neural tube give rise to Brgmann glial cells, specialized bipotential progenitors cells of the cerebellum. Differentiation includes the processes involved in commitment of a cell to a specific fate.

IEA

BP

GO:0060291

long-term synaptic potentiation

A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse.

IEA

BP

GO:0060324

face development

The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.

IEA

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.

TAS

BP

GO:0060425

lung morphogenesis

The process in which the anatomical structures of the lung are generated and organized.

IEA

BP

GO:0060440

trachea formation

The process pertaining to the initial formation of a trachea from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the trachea is recognizable. The trachea is the portion of the airway that attaches to the bronchi as it branches.

IEA

BP

GO:0060716

labyrinthine layer blood vessel development

The process whose specific outcome is the progression of a blood vessel of the labyrinthine layer of the placenta over time, from its formation to the mature structure. The embryonic vessels grow through the layer to come in close contact with the maternal blood supply.

IEA

BP

GO:0061308

cardiac neural crest cell development involved in heart development

The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the development of the heart.

IEA

BP

GO:0070371

ERK1 and ERK2 cascade

An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (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.

IDA|TAS

BP

GO:0070849

response to epidermal growth 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 an epidermal growth factor stimulus.

IDA

BP

GO:0072584

caveolin-mediated endocytosis

An endocytosis process that begins when material is taken up into plasma membrane caveolae, which then pinch off to form endocytic caveolar carriers.

TAS

BP

GO:0090170

regulation of Golgi inheritance

Any process that modulates the rate, frequency or extent of Golgi inheritance. Golgi inheritance is the partitioning of Golgi apparatus between daughter cells at cell division.

TAS

BP

GO:0097011

cellular response to granulocyte macrophage colony-stimulating 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 granulocyte macrophage colony-stimulating factor stimulus.

IEA

BP

GO:1900034

regulation of cellular response to heat

Any process that modulates the frequency, rate or extent of cellular response to heat.

TAS

BP

GO:1904355

positive regulation of telomere capping

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

IMP

BP

GO:2000641

regulation of early endosome to late endosome transport

Any process that modulates the frequency, rate or extent of early endosome to late endosome transport.

TAS

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|TAS

CC

GO:0005654

nucleoplasm

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

IDA|TAS

CC

GO:0005737

cytoplasm

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

IDA|ISS

CC

GO:0005739

mitochondrion

A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

TAS

CC

GO:0005769

early endosome

A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.

TAS

CC

GO:0005770

late endosome

A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.

TAS

CC

GO:0005794

Golgi apparatus

A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.

TAS

CC

GO:0005815

microtubule organizing center

An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.

IEA

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.

TAS

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.

TAS

CC

GO:0005925

focal adhesion

Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.

TAS

CC

GO:0015630

microtubule cytoskeleton

The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.

IDA

CC

GO:0030424

axon

The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.

IEA

CC

GO:0031143

pseudopodium

A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding.

IEA

CC

GO:0032839

dendrite cytoplasm

All of the contents of a dendrite, excluding the surrounding plasma membrane.

IEA

CC

GO:0043204

perikaryon

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

IEA

CC

GO:0043234

protein complex

A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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

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.

ISS

MF

GO:0001784

phosphotyrosine binding

Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein.

IEA

MF

GO:0003677

DNA binding

Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

IEA

MF

GO:0004674

protein serine/threonine kinase activity

Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.

IDA|TAS

MF

GO:0004707

MAP kinase activity

Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli.

TAS

MF

GO:0005515

protein binding

Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

IPI

MF

GO:0005524

ATP binding

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

IEA

MF

GO:0008134

transcription factor binding

Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.

IEA

MF

GO:0008353

RNA polymerase II carboxy-terminal domain kinase activity

Catalysis of the reaction: ATP + (DNA-directed RNA polymerase II) = ADP + phospho-(DNA-directed RNA polymerase II); phosphorylation occurs on residues in the carboxy-terminal domain (CTD) repeats.

ISS

MF

GO:0016301

kinase activity

Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.

TAS

MF

GO:0019902

phosphatase binding

Interacting selectively and non-covalently with any phosphatase.

IPI

MF

GO:0031435

mitogen-activated protein kinase kinase kinase binding

Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase kinase, any protein that can phosphorylate a MAP kinase kinase.

IEA

MF

GO:0042802

identical protein binding

Interacting selectively and non-covalently with an identical protein or proteins.

IEA