BP

GO:0000045

autophagosome assembly

The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.

IEA

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.

IEA

BP

GO:0000186

activation of MAPKK activity

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

IEA

BP

GO:0001568

blood vessel development

The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.

IEA

BP

GO:0001708

cell fate specification

The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.

IEA

BP

GO:0001756

somitogenesis

The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.

IEA

BP

GO:0001764

neuron migration

The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.

IEA

BP

GO:0001921

positive regulation of receptor recycling

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

IEA

BP

GO:0001947

heart looping

The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation.

IEA

BP

GO:0002244

hematopoietic progenitor cell differentiation

The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.

IEA

BP

GO:0002286

T cell activation involved in immune response

The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response.

IEA

BP

GO:0003407

neural retina development

The progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.

IEA

BP

GO:0006486

protein glycosylation

A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.

IEA

BP

GO:0006509

membrane protein ectodomain proteolysis

The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).

IDA

BP

GO:0006839

mitochondrial transport

Transport of substances into, out of or within a mitochondrion.

IEA

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:0006979

response to oxidative 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 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.

IEA

BP

GO:0007175

negative regulation of epidermal growth factor-activated receptor activity

Any process that stops, prevents, or reduces the frequency, rate or extent of EGF-activated receptor activity.

IEA

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.

IEA

BP

GO:0007220

Notch receptor processing

The series of successive proteolytic cleavages of the Notch protein, which result in an active form of the receptor.

TAS

BP

GO:0007613

memory

The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).

IEA

BP

GO:0009791

post-embryonic development

The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.

IEA

BP

GO:0015031

protein transport

The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

IEA

BP

GO:0015813

L-glutamate transport

The directed movement of L-glutamate, the L enantiomer anion of 2-aminopentanedioic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

IEA

BP

GO:0015871

choline transport

The directed movement of choline into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Choline (2-hydroxyethyltrimethylammonium) is an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine.

IEA

BP

GO:0016080

synaptic vesicle targeting

The process in which synaptic vesicles are directed to specific destination membranes, mediated by molecules at the vesicle membrane and target membrane surfaces.

IEA

BP

GO:0016337

single organismal cell-cell adhesion

The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.

IMP

BP

GO:0016485

protein processing

Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.

IDA

BP

GO:0021795

cerebral cortex cell migration

The orderly movement of cells from one site to another in the cerebral cortex.

IEA

BP

GO:0021870

Cajal-Retzius cell differentiation

The process in which a neuroblast acquires specialized structural and/or functional features of a Cajal-Retzius cell, one of a transient population of pioneering neurons in the cerebral cortex. These cells are slender bipolar cells of the developing marginal zone. One feature of these cells in mammals is that they express the Reelin gene.

IEA

BP

GO:0021904

dorsal/ventral neural tube patterning

The process in which the neural tube is regionalized in the dorsoventral axis.

IEA

BP

GO:0030326

embryonic limb morphogenesis

The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.

IEA

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.

IEA

BP

GO:0032469

endoplasmic reticulum calcium ion homeostasis

Any process involved in the maintenance of an internal steady state of calcium ions within the endoplasmic reticulum of a cell or between the endoplasmic reticulum and its surroundings.

IDA|IGI

BP

GO:0034205

beta-amyloid formation

The generation of beta-amyloid by cleavage of the amyloid precursor protein (APP).

IEA

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.

IEA

BP

GO:0042325

regulation of phosphorylation

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

IDA

BP

GO:0042987

amyloid precursor protein catabolic process

The chemical reactions and pathways resulting in the breakdown of amyloid precursor protein (APP), the precursor of beta-amyloid, a glycoprotein associated with Alzheimer's disease.

TAS

BP

GO:0043011

myeloid dendritic cell differentiation

The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin.

IEA

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.

IEA

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.

IDA

BP

GO:0043085

positive regulation of catalytic activity

Any process that activates or increases the activity of an enzyme.

IDA

BP

GO:0043393

regulation of protein binding

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

IEA

BP

GO:0043406

positive regulation of MAP kinase activity

Any process that activates or increases the frequency, rate or extent of MAP kinase activity.

IEA

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:0043589

skin morphogenesis

The process in which the anatomical structures of the skin are generated and organized. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner, sensitive and vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.

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.

IMP

BP

GO:0048167

regulation of synaptic plasticity

A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.

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:0048666

neuron development

The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.

IEA

BP

GO:0048705

skeletal system morphogenesis

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

IEA

BP

GO:0048854

brain morphogenesis

The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).

IEA

BP

GO:0050673

epithelial cell proliferation

The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances.

IEA

BP

GO:0050771

negative regulation of axonogenesis

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

IEA

BP

GO:0050820

positive regulation of coagulation

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

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:0051402

neuron apoptotic process

Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.

IEA

BP

GO:0051444

negative regulation of ubiquitin-protein transferase activity

Any process that stops, prevents, or reduces the frequency, rate or extent of ubiquitin transferase activity.

IEA

BP

GO:0051563

smooth endoplasmic reticulum calcium ion homeostasis

Any process involved in the maintenance of an internal steady state of calcium ions within the smooth endoplasmic reticulum of a cell or between the smooth endoplasmic reticulum and its surroundings.

IBA

BP

GO:0051966

regulation of synaptic transmission, glutamatergic

Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.

IEA

BP

GO:0060070

canonical 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, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.

IBA

BP

GO:0060075

regulation of resting membrane potential

Any process that modulates the establishment or extent of a resting potential, the electrical charge across the plasma membrane, with the interior of the cell negative with respect to the exterior. The resting potential is the membrane potential of a cell that is not stimulated to be depolarized or hyperpolarized.

IEA

BP

GO:0060999

positive regulation of dendritic spine development

Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.

IMP

BP

GO:0070588

calcium ion transmembrane transport

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

IEA

BP

GO:2000059

negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of protein ubiquitination involved in ubiquitin-dependent protein catabolic process.

IEA

BP

GO:2001234

negative regulation of apoptotic signaling pathway

Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway.

IEA

CC

GO:0000139

Golgi membrane

The lipid bilayer surrounding any of the compartments of the Golgi apparatus.

IEA

CC

GO:0000776

kinetochore

A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.

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:0005640

nuclear outer membrane

The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.

IDA

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.

IDA

CC

GO:0005743

mitochondrial inner membrane

The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.

IEA

CC

GO:0005765

lysosomal membrane

The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.

IEA

CC

GO:0005783

endoplasmic reticulum

The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

IDA

CC

GO:0005789

endoplasmic reticulum membrane

The lipid bilayer surrounding the endoplasmic reticulum.

IEA

CC

GO:0005790

smooth endoplasmic reticulum

The smooth endoplasmic reticulum (smooth ER or SER) has no ribosomes attached to it. The smooth ER is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER.

IDA

CC

GO:0005791

rough endoplasmic reticulum

The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.

IDA

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.

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: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.

IDA

CC

GO:0005887

integral component of plasma membrane

The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

IDA

CC

GO:0009986

cell surface

The external part of the cell wall and/or plasma membrane.

IEA

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:0016021

integral component of membrane

The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

TAS

CC

GO:0016235

aggresome

An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules.

IDA

CC

GO:0030054

cell junction

A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.

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:0030426

growth cone

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

IEA

CC

GO:0031410

cytoplasmic vesicle

A vesicle found in the cytoplasm of a cell.

IEA

CC

GO:0031594

neuromuscular junction

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

IEA

CC

GO:0031965

nuclear membrane

Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.

IDA

CC

GO:0035253

ciliary rootlet

A cytoskeleton-like structure, originating from the basal body at the proximal end of a cilium, and extending proximally toward the cell nucleus. Rootlets are typically 80-100 nm in diameter and contain cross striae distributed at regular intervals of approximately 55-70 nm.

IEA

CC

GO:0043025

neuronal cell body

The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.

IEA

CC

GO:0043198

dendritic shaft

Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines.

IEA

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.

IDA

CC

GO:0070765

gamma-secretase complex

A protein complex that has aspartic-type endopeptidase activity, and contains a catalytic subunit, presenilin (PS), that is a prototypical member of the GxGD-type aspartyl peptidases. The complex also contains additional subunits, including nicastrin, APH-1, PEN-2, and a regulatory subunit, CD147. Gamma-secretase cleaves several transmembrane proteins including the cell surface receptor Notch and the beta-amyloid precursor protein.

IDA

CC

GO:0098793

presynapse

The part of a synapse that is part of the presynaptic cell.

IEA

MF

GO:0004175

endopeptidase activity

Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.

IDA

MF

GO:0004190

aspartic-type endopeptidase activity

Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.

IEA

MF

GO:0005262

calcium channel activity

Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.

IMP

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:0008013

beta-catenin binding

Interacting selectively and non-covalently with the beta subunit of the catenin complex.

IPI

MF

GO:0030165

PDZ domain binding

Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.

IPI

MF

GO:0045296

cadherin binding

Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion.

IBA