viral transcription

definition: The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.


intracellular transport of virus

category: biolink:BiologicalProcess biolink:Occurrent biolink:OntologyClass biolink:BiologicalProcessOrActivity biolink:BiologicalEntity biolink:ThingWithTaxon biolink:NamedThing biolink:PhysicalEssenceOrOccurrent

definition: The directed movement of a virus, or part of a virus, within the host cell.


name: regulation of type I interferon-mediated signaling pathway

definition: Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway.


name: type I interferon-mediated signaling pathway

category: biolink:Pathway biolink:OntologyClass biolink:BiologicalProcess biolink:Occurrent biolink:BiologicalProcessOrActivity biolink:BiologicalEntity biolink:ThingWithTaxon biolink:NamedThing biolink:PhysicalEssenceOrOccurrent

definition: The series of molecular signals initiated by type I interferon binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.


mRNA metabolic process

definition: The chemical reactions and pathways involving mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.


name: mRNA 3'-end processing by stem-loop binding and cleavage

definition: Any mRNA 3'-end processing that involves the binding to and cleavage of a stem-loop structure. For example, histone mRNAs contain a highly conserved stem-loop sequence at the 3' end of the mRNA with a 6 base pairs (bp) stem and a 4-nt loop. The mRNA is cleaved between these two elements, after the fourth or fifth nucleotide, which is typically an adenosine.


translational initiation

definition: The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.


PKR/eIFalpha signaling

definition: An intracellular signaling cassette that starts with activation and autophosphorylation of PKR (also known as EIF2AK2), which phosphorylates proteins including the translation initiation factor eIF2 to inhibit translation. PKR is activated by stress signals and during the antiviral response, activated by binding to viral double-stranded RNA (dsRNA) leading to inhibition of protein synthesis during viral infection.


name: antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent

definition: The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.


name: antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent

definition: The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a pathway not requiring TAP (transporter associated with antigen processing). The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell. Class I here refers to classical class I molecules.


name: antigen processing and presentation of exogenous peptide antigen via MHC class I

definition: The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules.


protein polyubiquitination

definition: Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.


name: antigen processing and presentation of peptide antigen via MHC class I

definition: The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.


innate immune response

definition: Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.


mitotic cytokinesis

definition: A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.


amyloid fibril formation

definition: The generation of amyloid fibrils, insoluble fibrous protein aggregates exhibiting beta sheet structure, from proteins.


viral life cycle

definition: A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.


viral process

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


viral genome maturation

definition: The processes involved in creating a mature, stable viral genome. Begins after genome replication with a newly synthesized nucleic acid and ends when the genome is ready to be packaged. Includes the addition of proteins to the newly synthesized genome, and DNA repair processes.


name: receptor-mediated endocytosis of virus by host cell

definition: Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.


name: fusion of virus membrane with host plasma membrane

definition: Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.


uncoating of virus

definition: The process by which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.


name: symbiont-mediated suppression of host mRNA processing

definition: A process in which a symbiont inhibits or disrupts mRNA processing in its host. mRNA processing is the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide. The host is defined as the larger of the organisms involved in a symbiotic interaction.


name: modulation by virus of host cellular process

definition: The process in which a virus effects a change in the processes and activities of its host organism.


inflammatory cell apoptotic process

definition: Any apoptotic process in an inflammatory cell, any cell participating in the inflammatory response to a foreign substance e.g. neutrophil, macrophage.


viral release from host cell

definition: The dissemination of mature viral particles from a host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.


virion assembly

definition: A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.


viral genome packaging

definition: The encapsulation of the viral genome within the capsid.


name: intracellular transport of viral protein in host cell

definition: The directed movement of a viral protein within the host cell.


viral protein processing

definition: Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.


name: transcription elongation by RNA polymerase II

definition: The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.


name: positive regulation of viral transcription

definition: Any process that activates or increases the frequency, rate or extent of viral transcription.


name: transcription initiation at RNA polymerase II promoter

definition: A transcription initiation process that takes place at a RNA polymerase II gene promoter. Messenger RNAs (mRNA) genes, as well as some non-coding RNAs, are transcribed by RNA polymerase II.


name: termination of RNA polymerase II transcription

definition: A transcription termination process that completes the production of a primary RNA polymerase II transcript.


name: snRNA transcription by RNA polymerase II

definition: The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.


name: regulation of transcription by RNA polymerase II

definition: Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II.


name: negative regulation of Notch signaling pathway

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


BMP signaling pathway

definition: The 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 the regulation of a downstream cellular process, e.g. transcription.


regulation of Wnt signaling pathway

definition: Any process that modulates the frequency, rate or extent of the activity of the Wnt signal transduction pathway.


name: regulation of keratinocyte differentiation

definition: Any process that modulates the frequency, rate or extent of keratinocyte differentiation.


name: regulation of myeloid cell differentiation

definition: Any process that modulates the frequency, rate or extent of myeloid cell differentiation.


name: regulation of cytokine-mediated signaling pathway

definition: Any process that modulates the frequency, rate or extent of the cytokine mediated signaling pathway.


name: regulation of B cell receptor signaling pathway

definition: Any process that modulates the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a B cell.


name: regulation of hematopoietic stem cell differentiation

definition: Any process that modulates the frequency, rate or extent of hematopoietic stem cell differentiation.


name: regulation of intracellular estrogen receptor signaling pathway

definition: Any process that modulates the frequency, rate or extent of the activity of an intracellular estrogen receptor signaling pathway.


name: regulation of megakaryocyte differentiation

definition: Any process that modulates the frequency, rate or extent of megakaryocyte differentiation.


name: regulation of regulatory T cell differentiation

definition: Any process that modulates the frequency, rate or extent of differentiation of regulatory T cells.


name: regulation of bicellular tight junction assembly

definition: Any process that modulates the frequency, rate or extent of tight junction assembly.


hippo signaling

definition: An intracellular signaling cascade that starts with the activation of hippo (STK4/MST1 and STK3/MST2 in mammals and hpo kinase in Drosophila). Hippo then phosphorylates LATS1/2, which in turn phosphoylates the transcriptional co-activator YAP1 (yki in Drosophila), leading to its cytosolic retention and/or degradation.


name: negative regulation of G0 to G1 transition

definition: A cell cycle process that stops, prevents, or reduces the rate or extent of the transition from the G0 quiescent state to the G1 phase.


name: regulation of transcription initiation by RNA polymerase II

definition: Any process that modulates the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.


transcription by RNA polymerase II

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


defense response to virus

definition: Reactions triggered in response to the presence of a virus that act to protect the cell or organism.


RNA metabolic process

definition: The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.


definition: The series of molecular signals initiated by interleukin-17 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


viral translation

definition: A process by which viral mRNA is translated into viral protein, using the host cellular machinery.


name: induction by virus of host cell-cell fusion

definition: The process of syncytia-forming cell-cell fusion, caused by a virus.


translational elongation

definition: The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.


mitotic M phase

definition: A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle.


name: anaphase-promoting complex-dependent catabolic process

definition: 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, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.


name: regulation of anaphase-promoting complex-dependent catabolic process

definition: Any process that modulates the frequency, rate or extent of anaphase-promoting complex-dependent catabolic process.


regulation of exit from mitosis

definition: Any process involved in the progression from anaphase/telophase to G1 that is associated with a conversion from high to low mitotic CDK activity.


mitotic cell cycle

definition: Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.


CENP-A containing chromatin assembly

definition: The formation of chromatin containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.


name: negative regulation of DNA recombination at telomere

definition: Any process that stops, prevents, or reduces the frequency, rate or extent of genetic recombination within the telomere.


name: response to mitochondrial depolarisation

definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) in response to the depolarization of one or more mitochondria.


regulation of cellular response to heat

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


cellular response to heat

definition: 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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.


name: cellular response to amino acid starvation

definition: 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 deprivation of amino acids.


glycerol transmembrane transport

definition: The directed movement of glycerol across a membrane. Glycerol is 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.


water transport

definition: The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.


renal water homeostasis

definition: Renal process involved in the maintenance of an internal steady state of water in the body.


name: mitochondrial calcium ion transmembrane transport

definition: The process in which a calcium ion (Ca2+) is transported across a mitochondrial membrane, into or out of the mitochondrion.


lipid transport

definition: The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.


transmembrane transport

definition: The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.


zinc ion transmembrane transport

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


myo-inositol transport

definition: The directed movement of myo-inositol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Myo-inositol is 1,2,3,4,5/4,6-cyclohexanehexol, a growth factor for animals and microorganisms.


glucose transmembrane transport

definition: The process in which glucose is transported across a membrane.


hexose transmembrane transport

definition: The process in which hexose is transported across a membrane. Hexoses are aldoses with a chain of six carbon atoms in the molecule.


name: sodium-independent organic anion transport

definition: The directed, sodium-independent, movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.


long-chain fatty acid transport

definition: The directed movement of a long-chain fatty acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons.


name: very-low-density lipoprotein particle assembly

definition: The non-covalent aggregation and arrangement of proteins and lipids in the liver to form a very-low-density lipoprotein particle.


name: high-density lipoprotein particle assembly

definition: The non-covalent aggregation and arrangement of proteins and lipids to form a high-density lipoprotein particle.


plasma lipoprotein particle assembly

definition: The non-covalent aggregation and arrangement of proteins and lipids to form a plasma lipoprotein particle.


name: low-density lipoprotein particle remodeling

definition: The acquisition, loss or modification of a protein or lipid within a low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.


name: high-density lipoprotein particle remodeling

definition: The acquisition, loss or modification of a protein or lipid within a high-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.


plasma lipoprotein particle remodeling

definition: The acquisition, loss or modification of a protein or lipid within a plasma lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the esterification of cholesterol by phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT).


chylomicron remnant clearance

definition: The process in which a chylomicron remnant is removed from the blood via receptor-mediated endocytosis into liver cells and its constituent parts degraded.


name: high-density lipoprotein particle clearance

definition: The process in which a high-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.


name: very-low-density lipoprotein particle clearance

definition: The process in which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.


name: low-density lipoprotein particle receptor catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of a low-density lipoprotein particle receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.


name: low-density lipoprotein particle clearance

definition: The process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.


plasma lipoprotein particle clearance

definition: The process in which a lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.


name: plasma lipoprotein particle organization

definition: A protein-lipid complex subunit organization process that results in the formation, disassembly, or alteration of a plasma lipoprotein particle. A plasma lipoprotein particle is a spherical particle with a hydrophobic core of triglycerides and/or cholesterol esters, surrounded by an amphipathic monolayer of phospholipids, cholesterol and apolipoproteins.


oxygen transport

definition: The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.


calcium ion transmembrane transport

definition: 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.


monoatomic ion transmembrane transport

definition: A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.


transport

definition: 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 or a transporter complex, a pore or a motor protein.


xenobiotic metabolic process

definition: The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.

description: The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.


name: 3'-phosphoadenosine 5'-phosphosulfate metabolic process

definition: The chemical reactions and pathways involving 3'-phosphoadenosine 5'-phosphosulfate, a naturally occurring mixed anhydride. It is an intermediate in the formation of a variety of sulfo compounds in biological systems.


glutathione biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins.


name: glutathione derivative biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of glutathione derivative.


UDP-glucuronate biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of UDP-glucuronate, a substance composed of glucuronic acid in glycosidic linkage with uridine diphosphate.


cellular glucuronidation

definition: The modification of an organic chemical by the conjugation of glucuronic acid. The substances resulting from glucuronidation are known as glucuronosides (or glucuronides) and are often much more water-soluble than the non-glucuronic acid-containing precursor.


name: regulation of DNA-binding transcription factor activity

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


name: cellular response to steroid hormone stimulus

definition: 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 steroid hormone stimulus.


name: endoplasmic reticulum unfolded protein response

definition: The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.


PERK-mediated unfolded protein response

definition: The series of molecular signals mediated by the endoplasmic reticulum membrane stress sensor PERK (PKR-like ER kinase). Begins with activation of PERK in response to endoplasmic reticulum (ER) stress and ends with regulation of a downstream cellular process, e.g. transcription. The main substrate of PERK is the translation initiation factor eIF2alpha. Serine-phosphorylation of eIF2alpha by PERK inactivates eIF2alpha and inhibits general protein translation. In addition, eIF2alpha phosphorylation preferentially increases the translation of selective mRNAs such as ATF4 (activating transcription factor 4), which up regulates a subset of UPR genes required to restore folding capacity.


IRE1-mediated unfolded protein response

definition: The series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.


ATF6-mediated unfolded protein response

definition: The series of molecular signals mediated by the endoplasmic reticulum membrane stress sensor ATF6 (activating transcription factor 6). Begins with activation of ATF6 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. Under conditions of endoplasmic reticulum stress, ATF6 translocates to the Golgi where it is processed by proteases to release a cytoplasmic domain (ATF6f), which operates as a transcriptional activator of many genes required to restore folding capacity.


name: regulation of eIF2 alpha phosphorylation by heme

definition: Any process that modulates the rate, frequency, or extent of eIF2 alpha phosphorylation as a result of heme levels.


cellular response to stress

definition: 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 the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).


response to metal ion

definition: 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 metal ion stimulus.


cellular response to stimulus

definition: 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. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.


circadian rhythm

definition: Any biological process in an organism that recurs with a regularity of approximately 24 hours.


embryo development

definition: The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.


paraxial mesoderm formation

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


axial mesoderm formation

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


intermediate mesoderm formation

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


epithelial to mesenchymal transition

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


Wnt signaling pathway

definition: The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of a target cell and ending with a change in cell state.


neural plate pattern specification

definition: The developmental process that results in the creation of defined areas or spaces within the neural plate to which cells respond and eventually are instructed to differentiate.


endoderm formation

definition: The formation of the endoderm during gastrulation.


primitive streak formation

definition: The developmental process pertaining to the initial formation of the primitive streak from unspecified parts. The primitive streak is a ridge of cells running along the midline of the embryo where the mesoderm ingresses. It defines the anterior-posterior axis.


posterior neural plate formation

definition: The formation of posterior end of the flat, thickened layer of ectodermal cells known as the neural plate.


lateral mesoderm formation

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


anterior neural plate formation

definition: The formation of anterior end of the flat, thickened layer of ectodermal cells known as the neural plate.


name: positive regulation of muscle cell differentiation

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


granulocyte differentiation

definition: The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.


name: maternal-to-zygotic transition of gene expression

definition: Any process that modulates the frequency, rate or extent of gene expression by which developmental control passes from the maternal genome to the zygotic genome.


name: epigenetic programming in the zygotic pronuclei

definition: The global programming of epigenetic modifications in the zygote following fertilization. The paternal genome undergoes active DNA demethylation before the first cell division, while the adjacent maternal genome is protected from this process.


nephric duct formation

definition: The developmental process pertaining to the initial formation of a nephric duct. A nephric duct is a tube that drains a primitive kidney.


name: somatic stem cell population maintenance

definition: Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.


male gonad development

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


Rac protein signal transduction

definition: An intracellular signaling cassette in which a small monomeric GTPase of the Rac subfamily relays a signal.


name: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

definition: The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.


ephrin receptor signaling pathway

definition: The series of molecular signals initiated by ephrin binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription.


white fat cell differentiation

definition: The process in which a relatively unspecialized cell acquires specialized features of a white adipocyte, an animal connective tissue cell involved in energy storage. White adipocytes have cytoplasmic lipids arranged in a unique vacuole.


name: regulation of brown fat cell differentiation

definition: Any process that modulates the rate, frequency, or extent of brown fat cell differentiation. Brown fat cell differentiation is the process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.


name: regulation of adipose tissue development

definition: Any process that modulates the frequency, rate or extent of adipose tissue development.


cornification

definition: A type of programmed cell death that occurs in the epidermis, morphologically and biochemically distinct from apoptosis. It leads to the formation of corneocytes, i.e. dead keratinocytes containing an amalgam of specific proteins (e.g., keratin, loricrin, SPR and involucrin) and lipids (e.g., fatty acids and ceramides), which are necessary for the function of the cornified skin layer (mechanical resistance, elasticity, water repellence and structural stability).


heart formation

definition: The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable.


endocrine pancreas development

definition: The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin.


name: regulation of type B pancreatic cell development

definition: Any process that modulates the frequency, rate or extent of pancreatic B cell development.


keratinocyte development

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


lipid digestion

definition: The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested lipids into components that may be easily absorbed and directed into metabolism.


polysaccharide digestion

definition: The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested polysaccharides into components that may be easily absorbed and directed into metabolism.


blood coagulation, extrinsic pathway

definition: A protein activation cascade that contributes to blood coagulation and consists of the self-limited process linking exposure and activation of tissue factor to the activation of clotting factor X.


blood coagulation, intrinsic pathway

definition: A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.


blood coagulation

definition: The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.


name: peptidyl-lysine modification to peptidyl-hypusine

definition: The modification of peptidyl-lysine to form hypusine, peptidyl-N6-(4-amino-2-hydroxybutyl)-L-lysine.


signal peptide processing

definition: The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.


peptidyl-glutamic acid carboxylation

definition: The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.


name: protein histidyl modification to diphthamide

definition: The modification of peptidyl-histidine to 2'-(3-carboxamido-3-(trimethylammonio)propyl)-L-histidine, known as diphthamide, found in translation elongation factor EF-2. The process occurs in eukaryotes and archaea but not eubacteria.


vitamin K metabolic process

definition: The chemical reactions and pathways involving any of the forms of vitamin K, quinone-derived vitamins which are involved in the synthesis of blood-clotting factors in mammals. Vitamin K substances share a methylated naphthoquinone ring structure and vary in the aliphatic side chains attached to the molecule.


name: symbiont-mediated suppression of host innate immune response

definition: A process in which a symbiont inhibits or disrupts the normal execution of the innate immune response of the host organism, the host's first line of defense against infection. The host is defined as the larger of the organisms involved in a symbiotic interaction.


modulation by symbiont of host process

definition: The process in which a symbiont organism effects a change in the structure or processes of its host organism.


name: symbiont-mediated suppression of host defense-related programmed cell death

definition: Any process in which a symbiont stops, prevents, or reduces the frequency, rate or extent of defense-related programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.


name: symbiont-mediated perturbation of host defense response

definition: A process in which a symbiont interferes with the ability of the host to mount a defense in response to its presence. The host is defined as the larger of the organisms involved in a symbiotic interaction.


symbiont-mediated killing of host cell

definition: A process mediated by a symbiont that results in the death of a cell in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.


name: biological process involved in interaction with host

definition: An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.


response to antibiotic

definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.


response to bacterium

definition: 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 from a bacterium.


symbiont entry into host

definition: Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.


RNA-templated DNA biosynthetic process

definition: A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.


name: establishment of integrated proviral latency

definition: A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.


name: purine-containing compound transmembrane transport

definition: The process in which a purine-containing compound is transported across a membrane. A purine-containing compound is any compound that contains purine or a formal derivative thereof.


response to virus

definition: 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 from a virus.


name: negative regulation of inflammatory response to antigenic stimulus

definition: Any process that stops, prevents, or reduces the frequency, rate, or extent of an inflammatory response to an antigenic stimulus.


name: negative regulation of killing of cells of another organism

definition: Any process that stops, prevents, or reduces the frequency, rate or extent of the killing by an organism of cells in another organism.


negative regulation of cell killing

definition: Any process that stops, prevents, or reduces the frequency, rate or extent of cell killing.


phagocytosis

definition: A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.


name: adhesion of symbiont infection structure to host

definition: The attachment of an infection structure of the symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction.


positive regulation of cell killing

definition: Any process that activates or increases the frequency, rate or extent of cell killing.


name: purinergic nucleotide receptor signaling pathway

definition: The series of molecular signals initiated by an extracellular purine nucleotide binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription.


cell chemotaxis

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


name: biological process involved in interspecies interaction between organisms

definition: Any process evolved to enable an interaction with an organism of a different species.


response to cytokine

definition: 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 cytokine stimulus.


name: thiamine-containing compound metabolic process

definition: The chemical reactions and pathways involving thiamine (vitamin B1), and compounds derived from it.


vitamin B6 metabolic process

definition: The chemical reactions and pathways involving any of the vitamin B6 compounds: pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.


name: molybdopterin cofactor biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.


cobalamin transport

definition: The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.


cobalamin metabolic process

definition: The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.


folic acid metabolic process

definition: The chemical reactions and pathways involving folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.


L-ascorbic acid metabolic process

definition: The chemical reactions and pathways involving L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.


coenzyme A biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.


pantothenate metabolic process

definition: The chemical reactions and pathways involving pantothenate, the anion of pantothenic acid, the amide of beta-alanine and pantoic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.


riboflavin metabolic process

definition: The chemical reactions and pathways involving riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).


biotin metabolic process

definition: The chemical reactions and pathways involving biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid; the (+) enantiomer is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions.


water-soluble vitamin metabolic process

definition: The chemical reactions and pathways involving any of a diverse group of vitamins that are soluble in water.


glucocorticoid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol.


androgen biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics.


estrogen biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of estrogens, C18 steroid hormones that can stimulate the development of female sexual characteristics. Also found in plants.


mineralocorticoid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol.


name: C21-steroid hormone biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones.


steroid metabolic process

definition: The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.


prostanoid metabolic process

definition: The chemical reactions and pathways involving prostanoids, any compound based on or derived from the prostanoate structure.


ethanol catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of ethanol, CH3-CH2-OH, a colorless, water-miscible, flammable liquid produced by alcoholic fermentation.


cytochrome metabolic process

definition: The chemical reactions and pathways involving a cytochrome.


icosanoid metabolic process

definition: The chemical reactions and pathways involving icosanoids, any of a group of C20 polyunsaturated fatty acids.


sterol metabolic process

definition: The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.


fatty acid metabolic process

definition: The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.


vitamin metabolic process

definition: The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems.


aflatoxin metabolic process

definition: The chemical reactions and pathways involving aflatoxin, a fungal metabolite found as a contaminant in moldy grains that induces liver cancer. Aflatoxin induces a G to T transversion at codon 249 of p53, leading to its inactivation. Aflatoxin is converted to a chemical carcinogen by P450.


bile acid metabolic process

definition: The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.


bile acid and bile salt transport

definition: The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.


bile acid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile.


protein O-linked fucosylation

definition: The process of transferring a fucosyl group to a serine or threonine residues in a protein acceptor molecule, to form an O-linked protein-sugar linkage.


O-glycan processing

definition: The stepwise addition of carbohydrate or carbohydrate derivative residues to the initially added O-linked residue (usually GalNAc) to form a core O-glycan structure.


protein O-linked glycosylation

definition: A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the hydroxyl group of peptidyl-serine, peptidyl-threonine, peptidyl-hydroxylysine, or peptidyl-hydroxyproline, or via the phenol group of peptidyl-tyrosine, forming an O-glycan.


retinoid metabolic process

definition: The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.


name: G protein-coupled opsin signaling pathway

definition: A G protein-coupled receptor signaling pathway initiated by the excitation of rhodopsin by a photon, and ending with the regulation of a downstream cellular process.

description: A G protein-coupled receptor signaling pathway that starts with an opsin being activated by a photon, and ending with the light signal being trasmitted through the synapses. The signal can be transmitted via different Galpha subunits types: Go, Gs, Gq, and Gt.


name: regulation of opsin-mediated signaling pathway

definition: Any process that modulates the frequency, rate or extent of opsin-mediated signaling.


phototransduction, visible light

definition: The sequence of reactions within a cell required to convert absorbed photons from visible light into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.


base-excision repair, gap-filling

definition: Repair of the damaged strand by the combined action of an apurinic endouclease that degrades a few bases on the damaged strand and a polymerase that synthesizes a 'patch' in the 5' to 3' direction, using the undamaged strand as a template.


name: positive regulation of insulin secretion

definition: Any process that activates or increases the frequency, rate or extent of the regulated release of insulin.


name: negative regulation of insulin secretion

definition: Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin.


name: regulation of fatty acid biosynthetic process

definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils.


regulation of gene expression

definition: Any process that modulates 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 (protein or RNA).


name: positive regulation of cellular metabolic process

definition: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.


xylulose biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of xylulose, the ketopentose threo-2-pentulose.


protein kinase A signaling

definition: An intracellular signaling cassette that starts with the activation of protein kinase A (PKA), and ends with the regulation of a downstream cellular process, e.g. transcription. The PKA catalytic subunit (PKA-C) is normally present in a complex with its regulatory subunit, PKA-R. The inhibitory action of PKA-R is released upon cAMP binding, which results in the activation of PKA-C.


cellular response to glucagon stimulus

definition: 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 glucagon stimulus.


name: regulation of generation of precursor metabolites and energy

definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances.


serotonin catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.


dopamine catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline.


error-prone translesion synthesis

definition: The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.


error-free translesion synthesis

definition: The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.


translesion synthesis

definition: The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.


name: positive regulation of error-prone translesion synthesis

definition: Any process that activates or increases the frequency, rate or extent of error-prone translesion synthesis.


DNA alkylation repair

definition: The repair of alkylation damage in DNA, e.g. the removal of a non-physiological alkyl group from a nucleobase. This is usually mediated by DNA alkyltransferases.


DNA-templated DNA replication

definition: A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.


cyclooxygenase pathway

definition: The chemical reactions and pathways by which prostaglandins are formed from arachidonic acid, and in which prostaglandin-endoperoxide synthase (cyclooxygenase) catalyzes the committed step in the conversion of arachidonic acid to the prostaglandin-endoperoxides PGG2 and PGH2.


collagen catabolic process

definition: The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.


collagen fibril organization

definition: Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.


name: transcription initiation-coupled chromatin remodeling

definition: An epigenetic mechanism of regulation of gene expression that involves chromatin remodeling to capacitate gene expression by either modifying the chromatin fiber, the nucleosomal histones, or the DNA.


heterochromatin formation

definition: An epigenetic gene silencing mechanism in which chromatin is compacted into heterochromatin, resulting in a chromatin conformation refractory to transcription. This process starts with heterochromatin nucleation, its spreading, and ends with heterochromatin boundary formation.


name: chromosomal 5-methylcytosine DNA demethylation, oxidation pathway

definition: An epigenetic cytosine DNA demethylation pathway that starts with the enzymatic oxidation of the 5-methylcytosine (5meC) to generate 5-hydroxymethylcytosine (5hmC), which successively converted to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC).  A DNA glycosylase (e. g. TDG) recognizes the  intermediate bases 5fC and 5caC and excises the modified base to initiate its replacement with unmethylated cytosine through base excision repair.


name: retrotransposon silencing by heterochromatin formation

definition: A retrotransposon silencing mechanism involving heterochromatin assembly. Heterochromatin is a chromatin conformation that is refractory to transcription.


name: piRNA-mediated retrotransposon silencing by heterochromatin formation

definition: A retrotransposon silencing mechanism in which a Piwi-associated RNA (piRNA) triggers heterochromatin assembly. Heterochromatin is a chromatin conformation that is refractory to transcription.


rDNA heterochromatin formation

definition: The formation of heterochromatin at ribosomal DNA, characterized by the modified histone H3K9me3.


name: negative regulation of gene expression, epigenetic

definition: An epigenetic process that silences gene expression at specific genomic regions through chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or the cytosine DNA methylation.


name: termination of RNA polymerase I transcription

definition: A transcription termination process that completes the production of a ribosomal RNA transcript. RNAP I termination requires binding of a terminator protein to specific sequences downstream of the transcription unit.


name: transcription initiation at RNA polymerase I promoter

definition: A transcription initiation process that takes place at a RNA polymerase I gene promoter. Ribosomal RNAs (rRNA) genes are transcribed by RNA polymerase I.


transcription by RNA polymerase I

definition: The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.


name: transcription initiation at mitochondrial promoter

definition: A transcription initiation process that takes place at a promoter on the mitochondrial chromosome.


name: termination of mitochondrial transcription

definition: A transcription termination process that completes the production of a primary mitochondrial transcript.


mitochondrial transcription

definition: The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase.


siRNA processing

definition: A process leading to the generation of a functional small interfering RNA (siRNA). Includes the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides. May also include amplification of the siRNA by RNA-directed RNA polymerase.


miRNA metabolic process

definition: The chemical reactions and pathways involving miRNA, microRNA, a class of single-stranded RNA molecules of about 21-23 nucleotides in length, which regulates gene expression.


name: regulatory ncRNA-mediated post-transcriptional gene silencing

definition: A posttranscriptional gene silencing pathway in which regulatory RNAs elicit silencing of specific target genes, either by mRNA destabilization or inhibition of translation.


name: regulation of miRNA-mediated gene silencing

definition: A process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs).


piRNA processing

definition: A process leading to the generation of a functional piRNA. piRNAs (Piwi-associated RNAs) are a class of 24- to 30-nucleotide RNAs derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism.


tRNA decay

definition: The chemical reactions and pathways resulting in the breakdown of tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis.


name: regulatory ncRNA-mediated gene silencing

definition: A process in which an regulatory non-coding RNA molecule reduces expression of target genes. This can occur pre-transcriptionally by assembly of heterochromatin and prevention of transcription or co- or post-transcriptionally by targeting RNAs for degradation or by interfering with splicing or translation. This process starts once the inhibitory RNA molecule has been transcribed, and includes processing of the RNA such as cleavage, modifications, transport from the nucleus to the cytoplasm, loading onto the RISC complex, and the effect on transcription or translation.


transcription by RNA polymerase III

definition: The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.


name: transcription elongation by RNA polymerase III

definition: The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase III promoter by the addition of ribonucleotides catalyzed by RNA polymerase III.


name: termination of RNA polymerase III transcription

definition: A transcription termination process that completes the production of a primary RNA polymerase II transcript. RNA polymerase III has an intrinsic ability to terminate transcription upon incorporation of at least 4 contiguous U residues.


platelet activation

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


platelet degranulation

definition: The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.


fibrinolysis

definition: A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.


name: growth hormone receptor signaling pathway via JAK-STAT

definition: The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.


name: non-canonical NF-kappaB signal transduction

definition: An intracellular signaling cassette characterized by the NIK-dependent processing and activation of NF-kappaB. Begins with activation of the NF-kappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-kappa B2 protein (p100) leading to p100 processing and release of an active NF-kappaB (p52). The non-canonical NF-kappaB signaling pathway is generally activated by ligands of the TNF receptor superfamily, including lymphotoxin beta (LTB), CD40, OX40, RANK, TWEAK and B cell-activating factor (BAFF).


definition: The series of molecular signals initiated by interleukin-7 binding to its receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


definition: The series of molecular signals initiated by interleukin-27 binding to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


definition: The series of molecular signals initiated by interleukin-12 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


definition: The series of molecular signals initiated by interleukin-35 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


definition: The series of molecular signals initiated by interleukin-23 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


regulation of immune response

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


name: antigen processing and presentation of exogenous peptide antigen via MHC class II

definition: The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.


adaptive immune response

definition: An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).


myo-inositol phosphate transport

definition: The directed movement of any phosphorylated myo-inositol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.


inositol phosphate metabolic process

definition: The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.


triglyceride biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of a triglyceride, any triester of glycerol.


triglyceride catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of a triglyceride, any triester of glycerol.


triglyceride metabolic process

definition: The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.


regulation of lipid metabolic process

definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.


name: regulation of cholesterol biosynthetic process

definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol.


lipid droplet organization

definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lipid particle.


ketone body catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Ketone bodies can be used as an energy source as an alternative to glucose. Utilization of ketone bodies in peripheral tissues involves conversion of acetoacetate to acetoacetyl-CoA, which is then converted to two molecules of acetyl-CoA.


ketone body biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Biosynthesis involves the formation of hydroxymethylglutaryl-CoA, which is cleaved to acetate and acetyl-CoA.


cellular ketone body metabolic process

definition: The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism.


regulation of metabolic process

definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.


lipoxygenase pathway

definition: The chemical reactions and pathways by which an unsaturated fatty acid (such as arachidonic acid or linolenic acid) is converted to other compounds, and in which the first step is hydroperoxide formation catalyzed by lipoxygenase.


omega-hydroxylase P450 pathway

definition: The chemical reactions and pathways by which arachidonic acid is converted to other compounds initially by omega-hydroxylation.


leukotriene metabolic process

definition: The chemical reactions and pathways involving leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid.


hepoxilin metabolic process

definition: The chemical reactions and pathways involving hepoxilins, a class of bioactive icosanoids with roles in the regulation of cell physiology.


epoxygenase P450 pathway

definition: The chemical reactions and pathways by which arachidonic acid is converted to other compounds including epoxyeicosatrienoic acids and dihydroxyeicosatrienoic acids.


alpha-linolenic acid metabolic process

definition: The chemical reactions and pathways involving alpha-linolenic acid, an unsaturated omega-6 fatty acid that has the molecular formula C18H32O2.


linoleic acid metabolic process

definition: The chemical reactions and pathways involving linoleic acid, an unsaturated omega-6 fatty acid that has the molecular formula C18H32O2.


name: unsaturated fatty acid metabolic process

definition: The chemical reactions and pathways involving an unsaturated fatty acid, any fatty acid containing one or more double bonds between carbon atoms.


carnitine shuttle

definition: The transfer of acyl groups to and from acyl-CoA molecules to form O-acylcarnitine, which can exchange across the mitochondrial inner membrane with unacylated carnitine.


definition: Remodeling the acyl chains of phosphatidylethanolamine, through sequential deacylation and re-acylation reactions, to generate phosphatidylethanolamine containing different types of fatty acid acyl chains.


definition: The chemical reactions and pathways resulting in the formation of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.


phospholipid metabolic process

definition: The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.


definition: Remodeling the acyl chains of phosphatidylserine, through sequential deacylation and re-acylation reactions, to generate phosphatidylserine containing different types of fatty acid acyl chains.


phosphatidic acid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.


phospholipid transport

definition: The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Phospholipids are any lipids containing phosphoric acid as a mono- or diester.


phosphatidylserine biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of phosphatidylserines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of L-serine.


definition: The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.


definition: Remodeling the acyl chains of phosphatidylcholine, through sequential deacylation and re-acylation reactions, to generate phosphatidylcholine containing different types of fatty acid acyl chains.


cardiolipin biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of cardiolipin, 1,3-bis(3-phosphatidyl)glycerol.


acylglycerol acyl-chain remodeling

definition: Remodeling the acyl chains of an acylglycerol, through sequential deacylation and re-acylation reactions, to generate an acylglycerol containing different types of fatty acid acyl chains.


name: lysobisphosphatidic acid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of a lysobisphosphatidic acid. A lysobisphosphatidic acid is a lysophosphatidic acid having the unusual property of a phosphodiester moiety linked to positions sn-1 and sn1' of glycerol; and two additional fatty acids esterified to the glycerol head group.


cardiolipin acyl-chain remodeling

definition: Remodeling the acyl chains of premature (de novo synthesized) cardiolipin (1,3-bis(3-phosphatidyl)glycerol), through sequential deacylation and re-acylation reactions, to generate mature cardiolipin containing high-levels of unsaturated fatty acids.


definition: The chemical reactions and pathways resulting in the formation of phosphatidylglycerols, any of a class of phospholipids in which the phosphatidyl group is esterified to the hydroxyl group of glycerol.


definition: The chemical reactions and pathways resulting in the formation of phosphatidylethanolamine, any of a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine.


definition: Remodeling the acyl chains of phosphatidylglycerol, through sequential deacylation and re-acylation reactions, to generate phosphatidylglycerol containing different types of fatty acid acyl chains.


definition: Remodeling the acyl chains of phosphatidylinositol, through sequential deacylation and re-acylation reactions, to generate phosphatidylinositol containing different types of fatty acid acyl chains.


definition: The chemical reactions and pathways resulting in the formation of glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.


phospholipid translocation

definition: The movement of a phospholipid molecule from one leaflet of a membrane bilayer to the opposite leaflet.


glycerophospholipid catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.


ether lipid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of ether lipids, lipids that contain (normally) one lipid alcohol in ether linkage to one of the carbon atoms (normally C-1) of glycerol.


wax biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of wax, which includes C16 and C18 fatty acids.


lipid metabolic process

definition: The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.


name: long-chain fatty acid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of a long-chain fatty acid. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons.


lipoxin biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of a lipoxin. A lipoxin is a non-classic eicosanoid and signaling molecule that has four conjugated double bonds and is derived from arachidonic acid.


name: negative regulation of inflammatory response

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


vitamin E metabolic process

definition: The chemical reactions and pathways involving vitamin E, tocopherol, which includes a series of eight structurally similar compounds. Alpha-tocopherol is the most active form in humans and is a powerful biological antioxidant.


fat-soluble vitamin metabolic process

definition: The chemical reactions and pathways involving of any of a diverse group of vitamins that are soluble in organic solvents and relatively insoluble in water.


protein sumoylation

definition: The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxy-terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.


name: preassembly of GPI anchor in ER membrane

definition: The stepwise addition of the components of the GPI anchor on to phosphatidylinositol lipids in the endoplasmic reticulum membrane.


attachment of GPI anchor to protein

definition: A transamidation reaction that results in the cleavage of the polypeptide chain and the concomitant transfer of the GPI anchor to the newly formed carboxy-terminal amino acid of the anchored protein. The cleaved C-terminal contains the C-terminal GPI signal sequence of the newly synthesized polypeptide chain.


C-terminal protein lipidation

definition: The covalent attachment of a lipid group to the carboxy-terminus of a protein.


protein deubiquitination

definition: The removal of one or more ubiquitin groups from a protein.


name: chaperone mediated protein folding independent of cofactor

definition: The process of assisting in the correct noncovalent assembly of posttranslational proteins and does not depend on additional protein cofactors. This function occurs over one or more cycles of nucleotide-dependent binding and release.


name: 'de novo' post-translational protein folding

definition: The process of assisting in the correct noncovalent folding of newly formed polypeptides or folding intermediates of polypeptides that have exited the ribosome and/or have been stabilized and transferred by other chaperone proteins. This process could involve several cycles of ATP hydrolysis.


mitochondrial protein catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of a mitochondrial protein. This process is necessary to maintain the healthy state of mitochondria and is thought to occur via the induction of an intramitochondrial lysosome-like organelle that acts to eliminate the damaged oxidised mitochondrial proteins without destroying the mitochondrial structure.


peptide hormone processing

definition: The generation of a mature peptide hormone by posttranslational processing of a prohormone.


glucagon processing

definition: The formation of mature glucagon by proteolysis of the precursor proglucagon.


peptide metabolic process

definition: The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.


name: tRNA aminoacylation for protein translation

definition: The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, to be used in ribosome-mediated polypeptide synthesis.


translational termination

definition: The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).


protein metabolic process

definition: The chemical reactions and pathways involving a protein. Includes protein modification.


cytidine to uridine editing

definition: The conversion of a cytosine residue to uridine in an RNA molecule by deamination.


adenosine to inosine editing

definition: The conversion of an adenosine residue to inosine in an RNA molecule by deamination.


mRNA modification

definition: The covalent alteration of one or more nucleotides within an mRNA molecule to produce an mRNA molecule with a sequence that differs from that coded genetically.


regulation of mRNA stability

definition: Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.


mitochondrial tRNA processing

definition: The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group, in the mitochondrion.


tRNA modification

definition: The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.


mitochondrial tRNA modification

definition: The covalent alteration of one or more nucleotides within a mitochondrial tRNA molecule to produce a mitochondrial tRNA molecule with a sequence that differs from that coded genetically.


7-methylguanosine mRNA capping

definition: The sequence of enzymatic reactions by which the mRNA 5' cap structure, an inverted 7-methylguanosine linked via a 5'-5' triphosphate bridge (m7G(5')ppp(5')X) to the first transcribed residue, is added to a nascent transcript. Additional methylation can occur on the ribose sugars of the first and second nucleotides adjacent to the m7G nRNA cap. These methylations are often referred to as N6,2'-O-dimethyladenosine (m6,2A) and N6,2'-O-dimethylguanosine (m6,2G), respectively.


rRNA modification

definition: The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.


mRNA splicing, via spliceosome

definition: The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.


RNA splicing

definition: The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.


name: regulation of mitochondrial mRNA stability

definition: Any process that modulates the propensity of mitochondrial mRNA molecules to degradation. Includes processes that both stabilize and destabilize mitochondrial mRNAs.


mitochondrial RNA catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of RNA transcribed from the mitochondrial genome and occurring in the mitochondrion.


muscle contraction

definition: A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.


regulation of cardiac conduction

definition: Any process that modulates the frequency, rate or extent of cardiac conduction.


muscle filament sliding

definition: The sliding of actin thin filaments and myosin thick filaments past each other in muscle contraction. This involves a process of interaction of myosin located on a thick filament with actin located on a thin filament. During this process ATP is split and forces are generated.


name: cysteine biosynthetic process from serine

definition: The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine.


sulfur compound metabolic process

definition: The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.


mycothiol metabolic process

definition: The chemical reactions and pathways involving mycothiol, which consists of N-acetyl-L-cysteine linked to a pseudodisaccharide, D-glucosamine and myo-inositol. Mycothiol is produced in actinomycetes like mycobacteria and serves similar functions to glutathione.


mycothiol biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of mycothiol, which consists of N-acetyl-L-cysteine linked to a pseudodisaccharide, D-glucosamine and myo-inositol. Mycothiol is produced in actinomycetes like mycobacteria and serves similar functions to glutathione.


chorismate biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.


trehalose biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of trehalose, a disaccharide that consists of two molecules of glucose and is isomeric with sucrose.


lipid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.


potassium ion transmembrane transport

definition: A process in which a potassium ion is transported from one side of a membrane to the other.


name: positive regulation of potassium ion transmembrane transport

definition: Any process that activates or increases the frequency, rate or extent of potassium ion transmembrane transport.


name: ciliary basal body-plasma membrane docking

definition: The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane.


name: intraciliary transport involved in cilium assembly

definition: The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly.


mitochondrion organization

definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.


organelle organization

definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.


protein processing

definition: 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.


protein insertion into ER membrane

definition: The process that results in incorporation of a protein into an endoplasmic reticulum (ER) membrane. It depends on specific topogenic sequences of amino acids that ensure that a protein acquires the proper orientation during its insertion into the ER membrane.


protein import into peroxisome membrane

definition: The targeting of proteins into the peroxisomal membrane. The process is not well understood, but both signals and mechanism differ from those involved in peroxisomal matrix protein import.


germ cell development

definition: The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.


sperm-egg recognition

definition: The initial contact step made between the sperm plasma membrane and outer layer of the egg during fertilization.


acrosome reaction

definition: The discharge, by sperm, of a single, anterior secretory granule following the sperm's attachment to the zona pellucida of the oocyte. The process begins with the fusion of the outer acrosomal membrane with the sperm plasma membrane and ends with the exocytosis of the acrosomal contents into the zona pellucida.


single fertilization

definition: The union of male and female gametes to form a zygote.


name: multicellular organismal reproductive process

definition: The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.


sensory perception of sound

definition: The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.


name: regulation of small GTPase mediated signal transduction

definition: Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.


name: positive regulation of receptor signaling pathway via STAT

definition: Any process that activates or increases the frequency, rate or extent of receptor signaling pathway via STAT.


definition: The series of molecular signals initiated by erythropoietin (EPO) binding to the erythropoietin receptor (EPO-R) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


name: intracellular receptor signaling pathway

definition: The series of molecular signals initiated by a ligand binding to a receptor located within a cell.


name: hepatocyte growth factor receptor signaling pathway

definition: The series of molecular signals initiated by a ligand binding to a hepatocyte growth factor receptor, and ending with the regulation of a downstream cellular process, e.g. transcription.


name: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum

definition: The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.


post-Golgi vesicle-mediated transport

definition: The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles.


endosomal transport

definition: The directed movement of substances mediated by an endosome, a membrane-bounded organelle that carries materials enclosed in the lumen or located in the endosomal membrane.


membrane organization

definition: A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.


toll-like receptor 7 signaling pathway

definition: The series of molecular signals initiated by a ligand binding to the endolysosomal toll-like receptor 7.


toll-like receptor 21 signaling pathway

definition: The series of molecular signals initiated by a ligand binding to toll-like receptor 21.


toll-like receptor 15 signaling pathway

definition: The series of molecular signals initiated by a ligand binding to toll-like receptor 15.


name: negative regulation of innate immune response

definition: Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response.


MDA-5 signaling pathway

definition: The series of molecular signals initiated by the binding of dsRNA from another organism to the cytoplasmic pattern recognition receptor (PRR) MDA-5 (also known as IFIH1). MDA-5 detects RNA synthesized during viral replication or shed by non-viral pathogens, and triggers a signaling pathway to protect the host against infection, for example by inducing the expression of cytokines.


GMP biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.


'de novo' IMP biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.


AMP biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.


urate biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of urate, the anion of uric acid, 2,6,8-trioxypurine.


purine nucleobase metabolic process

definition: The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.


pyrimidine nucleobase metabolic process

definition: The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.


arginine metabolic process

definition: The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.


amino acid metabolic process

definition: The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.


glycolytic process

definition: The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.


small molecule metabolic process

definition: The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.


smoothened signaling pathway

definition: The series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.


name: cell surface receptor signaling pathway via JAK-STAT

definition: A cell surface receptor signaling pathway in which ligand binding causes the receptor to dimerize, bringing the receptor-associated JAKs into close proximity. The JAKs then phosphorylate and activate each other on tyrosine residues.This leads to the activation of associated STAT protein, causing the STATs to dissociate from the receptor, translocate to the nucleus. The pathway ends with regulation of target gene expression by STAT proteins.