BP

GO:0000165

MAPK cascade

An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.

IEA

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:0001710

mesodermal cell fate commitment

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

IEA

BP

GO:0002051

osteoblast fate commitment

The commitment of mesenchymal cells to the specific cell fate of an osteoblast. An osteoblast is a bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone.

IEA

BP

GO:0006366

transcription from RNA polymerase II promoter

The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).

IEA

BP

GO:0006954

inflammatory response

The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.

IEA

BP

GO:0007165

signal transduction

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

NAS

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.

NAS

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:0007276

gamete generation

The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.

IEA

BP

GO:0008285

negative regulation of cell proliferation

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

IEA

BP

GO:0009880

embryonic pattern specification

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

ISS

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:0030509

BMP signaling pathway

A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.

IDA|IMP|ISS|TAS

BP

GO:0030901

midbrain development

The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).

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:0031053

primary miRNA processing

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

TAS

BP

GO:0042592

homeostatic process

Any biological process involved in the maintenance of an internal steady state.

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: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.

IC|IDA

BP

GO:0051216

cartilage development

The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.

IEA

BP

GO:0060038

cardiac muscle cell proliferation

The expansion of a cardiac muscle cell population by cell division.

IEA

BP

GO:0060348

bone development

The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.

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.

ISS|NAS

BP

GO:0061036

positive regulation of cartilage development

Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.

IEA

BP

GO:1901522

positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus

Any positive regulation of transcription from RNA polymerase II promoter that is involved in cellular response to chemical stimulus.

ISS

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.

IEA

CC

GO:0005622

intracellular

The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

NAS

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|ISS|NAS|TAS

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.

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.

IEA

CC

GO:0005737

cytoplasm

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

IDA|ISS

CC

GO: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: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.

NAS

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:0071141

SMAD protein complex

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

NAS

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:0000979

RNA polymerase II core promoter sequence-specific DNA binding

Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.

IEA

MF

GO:0001077

transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific 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 (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.

IDA

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:0005057

receptor signaling protein activity

Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.

NAS

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: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: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.

TAS

MF

GO:0042802

identical protein binding

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

IPI

MF

GO:0042803

protein homodimerization activity

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

IEA

MF

GO:0046872

metal ion binding

Interacting selectively and non-covalently with any metal ion.

IEA

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:0070411

I-SMAD binding

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

IPI

MF

GO:0070878

primary miRNA binding

Interacting selectively and non-covalently with a primary microRNA (pri-miRNA) transcript, an RNA molecule that is processed into a short hairpin-shaped structure called a pre-miRNA and finally into a functional miRNA. Both double-stranded and single-stranded regions of a pri-miRNA are required for binding.

IEA