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:0000578

embryonic axis specification

The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo.

IEA

BP

GO:0001569

patterning of blood vessels

The process that regulates the coordinated growth and sprouting of blood vessels giving rise to the organized vascular system.

IC

BP

GO:0001658

branching involved in ureteric bud morphogenesis

The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.

IEA

BP

GO:0001701

in utero embryonic development

The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.

IEA

BP

GO:0001702

gastrulation with mouth forming second

A gastrulation process in which the initial invagination becomes the anus and the mouth forms second.

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:0001711

endodermal cell fate commitment

The cell differentiation process that results in commitment of a cell to become part of the endoderm.

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:0001837

epithelial to mesenchymal transition

A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.

TAS

BP

GO:0001840

neural plate development

The process whose specific outcome is the progression of the neural plate over time, from its formation to the mature structure. The neural plate is a flat, thickened layer of ectodermal cells. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system.

IEA

BP

GO:0002052

positive regulation of neuroblast proliferation

Any process that activates or increases the rate of neuroblast proliferation.

ISS

BP

GO:0002053

positive regulation of mesenchymal cell proliferation

The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells.

IEA

BP

GO:0002089

lens morphogenesis in camera-type eye

The process in which the anatomical structures of the lens are generated and organized. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.

IEA

BP

GO:0003266

regulation of secondary heart field cardioblast proliferation

Any process that modulates the frequency, rate or extent of cardioblast proliferation in the second heart field. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. The secondary heart field is the region of the heart that will form the majority of the mesodermal component of the right ventricle, the arterial pole (outflow tract) and the venous pole (inflow tract).

IEA

BP

GO:0003338

metanephros morphogenesis

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

IEA

BP

GO:0003340

negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis

Any process that decreases the rate, frequency or extent of the transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros.

IEA

BP

GO:0006351

transcription, DNA-templated

The cellular synthesis of RNA on a template of DNA.

IEA

BP

GO:0007155

cell adhesion

The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.

IMP

BP

GO:0007160

cell-matrix adhesion

The binding of a cell to the extracellular matrix via adhesion molecules.

IEA

BP

GO:0007223

Wnt signaling pathway, calcium modulating 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 leads to an increase in intracellular calcium and activation of protein kinase C (PKC).

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.

IEA

BP

GO:0007398

ectoderm development

The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation.

IEA

BP

GO:0007403

glial cell fate determination

The cell fate determination process in which a cell becomes capable of differentiating autonomously into a glial cell regardless of its environment; upon determination, the cell fate cannot be reversed.

IEA

BP

GO:0008285

negative regulation of cell proliferation

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

IDA

BP

GO:0009948

anterior/posterior axis specification

The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.

IEA

BP

GO:0009950

dorsal/ventral axis specification

The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.

IEA

BP

GO:0009954

proximal/distal pattern formation

The regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end).

IEA

BP

GO:0010718

positive regulation of epithelial to mesenchymal transition

Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.

IGI

BP

GO:0010909

positive regulation of heparan sulfate proteoglycan biosynthetic process

Any process that increases the rate, frequency or extent of heparan sulfate proteoglycan biosynthesis. Heparan sulfate proteoglycan biosynthetic processes are the chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues.

IMP

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.

IDA|TAS

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:0019827

stem cell population maintenance

The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.

TAS

BP

GO:0021819

layer formation in cerebral cortex

The detachment of cells from radial glial fibers at the appropriate time when they cease to migrate and form distinct layer in the cerebral cortex.

IEA

BP

GO:0022009

central nervous system vasculogenesis

The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes in the central nervous system. The capillary endothelial cells in the brain are specialized to form the blood-brain barrier.

IEA

BP

GO:0030316

osteoclast differentiation

The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.

IEA

BP

GO:0030521

androgen receptor signaling pathway

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

NAS

BP

GO:0030539

male genitalia development

The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure.

IEA

BP

GO:0030902

hindbrain development

The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium).

IEA

BP

GO:0030997

regulation of centriole-centriole cohesion

Any process that modulates the extent to which the two centrioles within a centrosome remain tightly paired; may be mediated by the assembly and disassembly of a proteinaceous linker.

IDA

BP

GO:0031016

pancreas development

The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes.

IEA

BP

GO:0031069

hair follicle morphogenesis

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

IEA

BP

GO:0031641

regulation of myelination

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

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.

IEA

BP

GO:0032331

negative regulation of chondrocyte differentiation

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

IEA

BP

GO:0032355

response to estradiol

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 estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.

IDA

BP

GO:0032481

positive regulation of type I interferon production

Any process that activates or increases 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:0033077

T cell differentiation in thymus

The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.

IEA

BP

GO:0033234

negative regulation of protein sumoylation

Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of SUMO groups to a protein.

IDA

BP

GO:0034333

adherens junction assembly

The aggregation, arrangement and bonding together of a set of components to form an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.

IMP

BP

GO:0034394

protein localization to cell surface

A process in which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane.

IMP

BP

GO:0035050

embryonic heart tube development

The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field.

IEA

BP

GO:0035112

genitalia morphogenesis

The process in which the anatomical structures of genitalia are generated and organized. The genitalia are the organs of reproduction or generation, external and internal.

IEA

BP

GO:0035115

embryonic forelimb morphogenesis

The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.

IEA

BP

GO:0035116

embryonic hindlimb morphogenesis

The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.

IEA

BP

GO:0035315

hair cell differentiation

The process in which a relatively unspecialized cell acquires specialized features of a hair cell.

TAS

BP

GO:0035411

catenin import into nucleus

The directed movement of a catenin protein from the cytoplasm into the nucleus.

TAS

BP

GO:0036023

embryonic skeletal limb joint morphogenesis

The process, occurring in the embryo, in which the anatomical structures of a skeletal limb joint are generated and organized. A skeletal limb joint is the connecting structure between the bones of a limb.

ISS

BP

GO:0042129

regulation of T cell proliferation

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

IEA

BP

GO:0042475

odontogenesis of dentin-containing tooth

The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel.

IEA

BP

GO:0042493

response to drug

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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.

IEP

BP

GO:0042733

embryonic digit morphogenesis

The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.

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.

IDA

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.

IEA

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:0043410

positive regulation of MAPK cascade

Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.

IEA

BP

GO:0043525

positive regulation of neuron apoptotic process

Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.

IDA

BP

GO:0044334

canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition

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 involved in the positive regulation of epithelial cell to mesenchymal cell transition.

IMP

BP

GO:0044336

canonical Wnt signaling pathway involved in negative regulation of apoptotic process

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 involved in the negative regulation of apoptotic process.

IMP

BP

GO:0045453

bone resorption

The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products.

IEA

BP

GO:0045603

positive regulation of endothelial cell differentiation

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

IEA

BP

GO:0045669

positive regulation of osteoblast differentiation

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

IEA

BP

GO:0045671

negative regulation of osteoclast differentiation

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

IEA

BP

GO:0045743

positive regulation of fibroblast growth factor receptor signaling pathway

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

IEA

BP

GO:0045765

regulation of angiogenesis

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

TAS

BP

GO:0045892

negative regulation of transcription, DNA-templated

Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.

IMP

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.

IDA|IMP

BP

GO:0045944

positive regulation of transcription from RNA polymerase II promoter

Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.

IDA|IMP|ISS|TAS

BP

GO:0045976

negative regulation of mitotic cell cycle, embryonic

Any process that stops, prevents or reduces the rate or extent of progression through the embryonic mitotic cell cycle.

ISS

BP

GO:0048096

chromatin-mediated maintenance of transcription

Maintenance of transcription by remodelling of chromatin into an 'open configuration'. Once established, this regulation is mitotically stable and is maintained over many cell divisions. It is also heritable.

IEA

BP

GO:0048145

regulation of fibroblast proliferation

Any process that modulates the frequency, rate or extent of multiplication or reproduction of fibroblast cells.

TAS

BP

GO:0048469

cell maturation

A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state.

IEA

BP

GO:0048489

synaptic vesicle transport

The directed movement of synaptic vesicles.

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:0048599

oocyte development

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

IEA

BP

GO:0048617

embryonic foregut morphogenesis

The process in which the anatomical structures of the foregut are generated and organized, during the embryonic phase.

IEA

BP

GO:0048643

positive regulation of skeletal muscle tissue development

Any process that activates, maintains or increases the rate of skeletal muscle tissue development.

IEA

BP

GO:0048660

regulation of smooth muscle cell proliferation

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

IMP

BP

GO:0048715

negative regulation of oligodendrocyte differentiation

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

IEA

BP

GO:0050767

regulation of neurogenesis

Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.

TAS

BP

GO:0050808

synapse organization

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).

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.

IMP

BP

GO:0051145

smooth muscle cell differentiation

The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell; smooth muscle lacks transverse striations in its constituent fibers and are almost always involuntary.

IEA

BP

GO:0051149

positive regulation of muscle cell differentiation

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

TAS

BP

GO:0051571

positive regulation of histone H3-K4 methylation

Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.

IC

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).

IEA

BP

GO:0060066

oviduct development

The reproductive developmental process whose specific outcome is the progression of an oviduct over time, from its formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism.

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.

IDA

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:0060441

epithelial tube branching involved in lung morphogenesis

The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.

IEA

BP

GO:0060479

lung cell differentiation

The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features of a mature cell found in the lung. Differentiation includes the processes involved in commitment of a cell to a specific fate.

IEA

BP

GO:0060484

lung-associated mesenchyme development

The biological process whose specific outcome is the progression of a lung-associated mesenchyme from an initial condition to its mature state. This process begins with the formation of lung-associated mesenchyme and ends with the mature structure. Lung-associated mesenchyme is the tissue made up of loosely connected mesenchymal cells in the lung.

IEA

BP

GO:0060492

lung induction

The close range interaction of two or more cells or tissues that causes the cells of the foregut to change their fates and specify the development of the lung.

IEA

BP

GO:0060742

epithelial cell differentiation involved in prostate gland development

The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell of the prostate gland.

IEA

BP

GO:0060769

positive regulation of epithelial cell proliferation involved in prostate gland development

Any process that increases the rate, frequency or extent of epithelial cell proliferation that contributes to the progression of the prostate gland over time.

IEA

BP

GO:0060789

hair follicle placode formation

The developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud.

IEA

BP

GO:0060916

mesenchymal cell proliferation involved in lung development

The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population that contributes to the progression of the lung over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.

IEA

BP

GO:0061154

endothelial tube morphogenesis

The process in which the anatomical structures of a tube are generated and organized from an endothelium. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.

IMP

BP

GO:0061198

fungiform papilla formation

The developmental process pertaining to the initial formation of a spongiform papilla from unspecified parts. The fungiform papilla is a mushroom-shaped papilla of the tongue.

IEA

BP

GO:0061324

canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation

The canonical Wnt signaling pathway that contributes to the modulation of the expansion of a population of cardiac outflow tract cells.

ISS

BP

GO:0061549

sympathetic ganglion development

The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure.

ISS

BP

GO:0061550

cranial ganglion development

The process whose specific outcome is the progression of a cranial ganglion over time, from its formation to the mature structure.

IEA

BP

GO:0070602

regulation of centromeric sister chromatid cohesion

Any process that modulates the frequency, rate or extent of sister chromatid cohesion in the centromeric region of a chromosome.

IMP

BP

GO:0071363

cellular response to growth factor stimulus

Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.

IMP

BP

GO:0071681

cellular response to indole-3-methanol

Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an indole-3-methanol stimulus.

IDA

BP

GO:0072033

renal vesicle formation

The developmental process pertaining to the initial formation of the renal vesicle from condensed mesenchymal cells. The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.

IEA

BP

GO:0072053

renal inner medulla development

The process whose specific outcome is the progression of the renal inner medulla over time, from its formation to the mature structure. The renal inner medulla is unique to mammalian kidneys and is the innermost region of the mammalian kidney.

IEA

BP

GO:0072054

renal outer medulla development

The process whose specific outcome is the progression of the renal outer medulla over time, from its formation to the mature structure. The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla.

IEA

BP

GO:0072079

nephron tubule formation

The developmental process pertaining to the initial formation of a nephron tubule from unspecified parts. A nephron tubule is an epithelial tube that is part of the nephron, the functional part of the kidney.

IEA

BP

GO:0072182

regulation of nephron tubule epithelial cell differentiation

Any process that modulates the frequency, rate or extent of nephron tubule epithelial cell differentiation.

ISS

BP

GO:0090279

regulation of calcium ion import

Any process that modulates the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.

IDA

BP

GO:1901215

negative regulation of neuron death

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

IEA

BP

GO:1904501

positive regulation of chromatin-mediated maintenance of transcription

Any process that activates or increases the frequency, rate or extent of chromatin-mediated maintenance of transcription.

IEA

BP

GO:1904793

regulation of euchromatin binding

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

IEA

BP

GO:1904796

regulation of core promoter binding

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

IEA

BP

GO:1904837

beta-catenin-TCF complex assembly

The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.

TAS

BP

GO:1904886

beta-catenin destruction complex disassembly

The disaggregation of a beta-catenin destruction complex into its constituent components.

TAS

BP

GO:1904888

cranial skeletal system development

The process whose specific outcome is the progression of a cranial skeletal system over time, from its formation to the mature structure. The cranial skeletal system is the skeletal subdivision of the head, and includes the skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.

IEA

BP

GO:1904948

midbrain dopaminergic neuron differentiation

The process in which a relatively unspecialized cell acquires the specialized features of a midbrain dopaminergic neuron.

ISS

BP

GO:1904954

canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation

Any canonical Wnt signaling pathway that is involved in midbrain dopaminergic neuron differentiation.

IC

BP

GO:1990403

embryonic brain development

The process occurring during the embryonic phase whose specific outcome is the progression of the brain over time, from its formation to the mature structure.

IEA

BP

GO:1990791

dorsal root ganglion development

The process whose specific outcome is the progression of a dorsal root ganglion over time, from its formation to the mature structure.

IEA

BP

GO:2000008

regulation of protein localization to cell surface

Any process that modulates the frequency, rate or extent of protein localization to the cell surface.

IDA

BP

GO:2000017

positive regulation of determination of dorsal identity

Any process that activates or increases the frequency, rate or extent of determination of dorsal identity.

IEA

BP

GO:2000144

positive regulation of DNA-templated transcription, initiation

Any process that activates or increases the frequency, rate or extent of DNA-templated transcription initiation.

IC

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:0000922

spindle pole

Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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:0005667

transcription factor complex

A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

IDA

CC

GO:0005719

nuclear euchromatin

The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.

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: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:0005829

cytosol

The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

IDA|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.

IDA

CC

GO:0005911

cell-cell junction

A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.

IDA

CC

GO:0005912

adherens junction

A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.

IDA

CC

GO:0005913

cell-cell adherens junction

An adherens junction which connects a cell to another cell.

IDA

CC

GO:0005916

fascia adherens

A cell-cell adherens junction that contains the transmembrane protein N-cadherin, which interacts with identical molecules from neighboring cells to form a tight mechanical intercellular link; forms a large portion of the intercalated disc, the structure at which myofibrils terminate in cardiomyocytes.

IEA

CC

GO:0005923

bicellular tight junction

An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.

IEA

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.

IDA

CC

GO:0005938

cell cortex

The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.

IDA

CC

GO:0016020

membrane

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

ISS

CC

GO:0016323

basolateral plasma membrane

The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.

IDA

CC

GO:0016328

lateral plasma membrane

The portion of the plasma membrane at the lateral side of the cell. In epithelial cells, lateral plasma membranes are on the sides of cells which lie at the interface of adjacent cells.

IDA

CC

GO:0016342

catenin complex

Complex of peripheral cytoplasmic proteins (alpha-, beta- and gamma-catenin) that interact with the cytoplasmic region of uvomorulin/E-cadherin to connect it to the actin cytoskeleton.

IDA

CC

GO:0016600

flotillin complex

A protein complex that contains flotillin-1 and flotillin-2, and may contain associated proteins. Flotillins associate into membrane microdomains resembling caveolae.

IEA

CC

GO:0030018

Z disc

Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.

IEA

CC

GO:0030027

lamellipodium

A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.

IEA

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|TAS

CC

GO:0030877

beta-catenin destruction complex

A cytoplasmic protein complex containing glycogen synthase kinase-3-beta (GSK-3-beta), the adenomatous polyposis coli protein (APC), and the scaffolding protein axin, among others; phosphorylates beta-catenin, targets it for degradation by the proteasome.

IDA

CC

GO:0031528

microvillus membrane

The portion of the plasma membrane surrounding a microvillus.

IEA

CC

GO:0032993

protein-DNA complex

A macromolecular complex containing both protein and DNA molecules.

IDA

CC

GO:0034750

Scrib-APC-beta-catenin complex

A protein complex that contains the Scribble protein (a cell polarity determinant), the tumor suppressor protein adenomatous polyposis coli (APC), and beta-catenin; may be involved in the control of cell proliferation.

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.

IDA

CC

GO:0045177

apical part of cell

The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.

IEA

CC

GO:0048471

perinuclear region of cytoplasm

Cytoplasm situated near, or occurring around, the nucleus.

IDA

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:0070369

beta-catenin-TCF7L2 complex

A protein complex that contains beta-catenin and TCF7L2 (TCF4), binds to the TCF DNA motif within a promoter element, and is involved in the regulation of WNT target gene transcription.

IDA

CC

GO:0071944

cell periphery

The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.

IDA

CC

GO:1990907

beta-catenin-TCF complex

A protein complex that contains beta-catenin and a member of the T-cell factor (TCF)/lymphoid enhancer binding factor (LEF) family of transcription factors.

IPI

CC

GO:1990909

Wnt signalosome

A multiprotein protein complex containing membrane-localized Wnt receptors and cytosolic protein complexes, which is capable of transmitting the Wnt signal. Contains at least a Wnt protein, LRP5 or LRP6, a member of the Frizzled (Fz) family, Axin and and a Dishevelled (DVL) protein.

NAS

MF

GO:0001085

RNA polymerase II transcription factor binding

Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.

IPI

MF

GO:0001102

RNA polymerase II activating transcription factor binding

Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.

IPI

MF

GO:0003690

double-stranded DNA binding

Interacting selectively and non-covalently with double-stranded DNA.

IEA

MF

GO:0003700

transcription factor activity, sequence-specific DNA binding

Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.

IEA

MF

GO:0003713

transcription coactivator activity

Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.

IDA|IMP

MF

GO:0004871

signal transducer activity

Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.

IEA

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: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.

IPI

MF

GO:0008134

transcription factor binding

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

IPI|TAS

MF

GO:0019899

enzyme binding

Interacting selectively and non-covalently with any enzyme.

IPI

MF

GO:0019900

kinase binding

Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.

IPI

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.

IEA

MF

GO:0019903

protein phosphatase binding

Interacting selectively and non-covalently with any protein phosphatase.

IPI

MF

GO:0030331

estrogen receptor binding

Interacting selectively and non-covalently with an estrogen receptor.

IPI

MF

GO:0035257

nuclear hormone receptor binding

Interacting selectively and non-covalently with a nuclear hormone receptor, a ligand-dependent receptor found in the nucleus of the cell.

IPI|TAS

MF

GO:0044212

transcription regulatory region DNA binding

Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.

IDA|ISS

MF

GO:0044325

ion channel binding

Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.

IPI

MF

GO:0045294

alpha-catenin binding

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

IPI

MF

GO:0045296

cadherin binding

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

IPI

MF

GO:0046332

SMAD binding

Interacting selectively and non-covalently with a SMAD signaling protein.

IPI

MF

GO:0050681

androgen receptor binding

Interacting selectively and non-covalently with an androgen receptor.

NAS

MF

GO:0070411

I-SMAD binding

Interacting selectively and non-covalently with an inhibitory SMAD signaling protein.

IPI

MF

GO:0070491

repressing transcription factor binding

Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.

IEA

MF

GO:0098641

cadherin binding involved in cell-cell adhesion

Any cadherin binding that occurs as part of the process of cell-cell adhesion.

IDA

MF

GO:1990188

euchromatin binding

Interacting selectively and non-covalently with euchromatin, a dispersed and relatively uncompacted form of chromatin.

IDA