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.

IDA|IMP|TAS

BP

GO:0001657

ureteric bud development

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

IEA

BP

GO:0001666

response to hypoxia

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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.

IMP

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:0001707

mesoderm formation

The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.

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:0001889

liver development

The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.

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:0002076

osteoblast development

The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone.

IEA

BP

GO:0002520

immune system development

The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.

IEA

BP

GO:0006351

transcription, DNA-templated

The cellular synthesis of RNA on a template of DNA.

IEA

BP

GO:0006357

regulation of transcription from RNA polymerase II promoter

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

IDA

BP

GO:0006810

transport

The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

IDA

BP

GO:0006919

activation of cysteine-type endopeptidase activity involved in apoptotic process

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

IMP

BP

GO:0006955

immune response

Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.

IMP

BP

GO:0007050

cell cycle arrest

A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).

IMP

BP

GO:0007179

transforming growth factor beta receptor signaling pathway

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

IDA|TAS

BP

GO:0007183

SMAD protein complex assembly

The aggregation, arrangement and bonding together of a set of components to form a protein complex that contains SMAD proteins.

IDA

BP

GO:0007492

endoderm development

The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.

IEA

BP

GO:0009880

embryonic pattern specification

The process that results in the patterns of cell differentiation that will arise in an embryo.

IEA

BP

GO:0010628

positive regulation of gene expression

Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.

IDA

BP

GO:0010694

positive regulation of alkaline phosphatase activity

Any process that increases the frequency, rate or extent of alkaline phosphatase activity, the catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.

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.

IDA|IMP

BP

GO:0016202

regulation of striated muscle tissue development

Any process that modulates the frequency, rate or extent of striated muscle development.

IEA

BP

GO:0017015

regulation of transforming growth factor beta receptor signaling pathway

Any process that modulates the frequency, rate or extent of activity of any TGF-beta receptor signaling pathway.

IMP

BP

GO:0019049

evasion or tolerance of host defenses by virus

Any process, either active or passive, by which a virus avoids or tolerates the effects of its host organism's defense(s). Host defenses may be induced by the presence of the virus or may be preformed (e.g. physical barriers). The host is defined as the larger of the organisms involved in a symbiotic interaction.

IDA

BP

GO:0023019

signal transduction involved in regulation of gene expression

Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another.

IEA

BP

GO:0030308

negative regulation of cell growth

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

IDA

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:0030501

positive regulation of bone mineralization

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

IEA

BP

GO:0030512

negative regulation of transforming growth factor beta receptor signaling pathway

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

TAS

BP

GO: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:0031053

primary miRNA processing

Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule.

TAS

BP

GO:0032332

positive regulation of chondrocyte differentiation

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

IEA

BP

GO:0032731

positive regulation of interleukin-1 beta production

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

IEA

BP

GO:0032909

regulation of transforming growth factor beta2 production

Any process that modulates the frequency, rate, or extent of production of transforming growth factor-beta2.

IMP

BP

GO:0032916

positive regulation of transforming growth factor beta3 production

Any process that activates or increases the frequency, rate, or extent of production of transforming growth factor-beta3.

IEA

BP

GO:0032924

activin receptor signaling pathway

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

IMP

BP

GO:0033689

negative regulation of osteoblast proliferation

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

IEA

BP

GO:0035413

positive regulation of catenin import into nucleus

Any process that increases the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus.

IEA

BP

GO:0038092

nodal signaling pathway

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

IMP

BP

GO:0042060

wound healing

The series of events that restore integrity to a damaged tissue, following an injury.

TAS

BP

GO:0042110

T cell activation

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.

IEA

BP

GO:0042177

negative regulation of protein catabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.

IEA

BP

GO:0042993

positive regulation of transcription factor import into nucleus

Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.

IDA

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.

IEA

BP

GO:0045216

cell-cell junction organization

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells.

IMP

BP

GO:0045429

positive regulation of nitric oxide biosynthetic process

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

IDA

BP

GO:0045599

negative regulation of fat cell differentiation

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

IDA

BP

GO:0045668

negative regulation of osteoblast differentiation

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

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.

IDA

BP

GO:0045930

negative regulation of mitotic cell cycle

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

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|TAS

BP

GO:0048340

paraxial mesoderm morphogenesis

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

IEA

BP

GO:0048589

developmental growth

The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.

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:0048701

embryonic cranial skeleton morphogenesis

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

IEA

BP

GO:0050678

regulation of epithelial cell proliferation

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

IEA

BP

GO:0050728

negative regulation of inflammatory response

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

IEA

BP

GO:0050776

regulation of immune response

Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.

IEA

BP

GO:0050821

protein stabilization

Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.

IEA

BP

GO:0050927

positive regulation of positive chemotaxis

Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.

IEA

BP

GO:0051098

regulation of binding

Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.

IEA

BP

GO:0051481

negative regulation of cytosolic calcium ion concentration

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

IDA

BP

GO:0051496

positive regulation of stress fiber assembly

Any process that activates or increases the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.

IEA

BP

GO:0051894

positive regulation of focal adhesion assembly

Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.

IEA

BP

GO:0060039

pericardium development

The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery.

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.

IEA

BP

GO:0060290

transdifferentiation

The conversion of a differentiated cell of one fate into a differentiated cell of another fate without first undergoing cell division or reversion to a more primitive or stem cell-like fate.

IEA

BP

GO:0060395

SMAD protein signal transduction

The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.

IEA

BP

GO:0061045

negative regulation of wound healing

Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.

IEA

BP

GO:0070306

lens fiber cell differentiation

The process in which a relatively unspecialized cell acquires specialized features of a lens fiber cell, any of the elongated, tightly packed cells that make up the bulk of the mature lens in the camera-type eye. The cytoplasm of a lens fiber cell is devoid of most intracellular organelles including the cell nucleus, and contains primarily crystallins, a group of water-soluble proteins expressed in vary large quantities.

IEA

BP

GO:0097191

extrinsic apoptotic signaling pathway

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

IMP

BP

GO:0097296

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

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

IEA

BP

GO:1901203

positive regulation of extracellular matrix assembly

Any process that activates or increases the frequency, rate or extent of extracellular matrix assembly.

IDA

BP

GO:1902895

positive regulation of pri-miRNA transcription from RNA polymerase II promoter

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

IMP

CC

GO:0000790

nuclear chromatin

The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.

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:0005637

nuclear inner membrane

The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.

IDA

CC

GO:0005654

nucleoplasm

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

IDA|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:0005737

cytoplasm

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

IDA

CC

GO:0005829

cytosol

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

TAS

CC

GO:0005886

plasma membrane

The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

IEA

CC

GO:0043235

receptor complex

Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

IMP

CC

GO:0071141

SMAD protein complex

A protein complex that consists of SMAD proteins; may be homomeric or heteromeric.

IDA

CC

GO:0071144

SMAD2-SMAD3 protein complex

A heteromeric SMAD protein complex that contains SMAD2 and SMAD3.

IDA

MF

GO:0000978

RNA polymerase II core promoter proximal region sequence-specific DNA binding

Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.

IDA

MF

GO:0000983

transcription factor activity, RNA polymerase II core promoter sequence-specific

Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to modulate transcription by Pol II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.

IDA|IMP

MF

GO:0000987

core promoter proximal region sequence-specific DNA binding

Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.

IDA

MF

GO:0000988

transcription factor activity, 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), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.

IDA

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: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.

IDA

MF

GO:0005160

transforming growth factor beta receptor binding

Interacting selectively and non-covalently with the transforming growth factor beta receptor.

IPI

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:0005518

collagen binding

Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).

IEA

MF

GO:0008013

beta-catenin binding

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

IEA

MF

GO:0008134

transcription factor binding

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

IPI

MF

GO:0008270

zinc ion binding

Interacting selectively and non-covalently with zinc (Zn) ions.

IDA

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.

IPI

MF

GO:0019902

phosphatase binding

Interacting selectively and non-covalently with any phosphatase.

IPI

MF

GO:0030618

transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity

A TGF-beta cytoplasmic mediator that is phosphorylated by a TGFbeta receptor and complexes with a common-partner mediator. The- heterocomplex translocates to the nucleus to regulate transcription.

IDA

MF

GO:0031490

chromatin DNA binding

Interacting selectively and non-covalently with DNA that is assembled into chromatin.

IEA

MF

GO:0031625

ubiquitin protein ligase binding

Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.

IPI

MF

GO:0035326

enhancer binding

Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.

IC

MF

GO:0042803

protein homodimerization activity

Interacting selectively and non-covalently with an identical protein to form a homodimer.

IPI

MF

GO:0043130

ubiquitin binding

Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.

IDA

MF

GO:0043425

bHLH transcription factor binding

Interacting selectively and non-covalently with any of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors, important regulatory components in transcriptional networks of many developmental pathways.

IPI

MF

GO:0043565

sequence-specific DNA binding

Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.

IDA

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

MF

GO:0046982

protein heterodimerization activity

Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.

IEA

MF

GO:0070410

co-SMAD binding

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

IPI

MF

GO:0070412

R-SMAD binding

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

IPI