iron-sulfur cluster assembly

The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.


regulation of mitochondrial membrane permeability involved in apoptotic process

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Any regulation of mitochondrial membrane permeability that is involved in apoptotic process.


regulation of Wnt signaling pathway

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


protein kinase C signaling

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

A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound.


cardiac muscle contraction

Muscle contraction of cardiac muscle tissue.


cardiac conduction

Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles.


actin binding

biolink:MolecularActivity biolink:BiologicalProcessOrActivity biolink:BiologicalEntity biolink:NamedThing biolink:Occurrent biolink:OntologyClass biolink:ThingWithTaxon biolink:PhysicalEssenceOrOccurrent

Binding to monomeric or multimeric forms of actin, including actin filaments.


cardiac muscle cell development

The process whose specific outcome is the progression of a cardiac muscle cell over time, from its formation to the mature state.


response to organic cyclic compound

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 organic cyclic compound stimulus.


branching involved in blood vessel morphogenesis

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


cardiac muscle cell contraction

The actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of a cardiac muscle cell.


muscle cell development

The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate.


miRNA-mediated gene silencing by inhibition of translation

An RNA interference pathway in which microRNAs (miRNAs) block the translation of target mRNAs into proteins. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically mediate repression of translation if the miRNA imperfectly base-pairs with the 3' untranslated regions of target mRNAs.


tissue remodeling

The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling.


positive regulation of transferase activity

Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.


galactose catabolic process via UDP-galactose

The chemical reactions and pathways resulting in the breakdown of galactose, via the intermediate UDP-galactose.


acetyl-CoA C-acyltransferase activity

Catalysis of the reaction: acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA.


response to calcium ion

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 calcium ion stimulus.


striated muscle contraction

A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. 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. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope.


myofibril assembly

Formation of myofibrils, the repeating units of striated muscle.


transmembrane transporter binding

Binding to a transmembrane transporter, a protein or protein complex that enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.


muscle contraction

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.


innervation

The process in which a nerve invades a tissue and makes functional synaptic connection within the tissue.


calcium ion import

The directed movement of calcium ions into a cell or organelle.


positive regulation of secondary heart field cardioblast proliferation

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


endocardial cushion development

The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.


negative regulation of MAPK cascade

Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade.


apoptotic process involved in heart morphogenesis

Any apoptotic process that contributes to the shaping of the heart.


peptidyl-tyrosine autophosphorylation

The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.


cardiac neural crest cell development involved in outflow tract morphogenesis

The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the shaping of the outflow tract.


cyclooxygenase pathway

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.


regulation of cytochrome-c oxidase activity

Any process that modulates the frequency, rate or extent of cytochrome-c oxidase activity.


cardiac myofibril assembly

The process whose specific outcome is the progression of the cardiac myofibril over time, from its formation to the mature structure. A cardiac myofibril is a myofibril specific to cardiac muscle cells.


smooth muscle cell migration

The orderly movement of a smooth muscle cell from one site to another, often during the development of a multicellular organism.


mitochondrial respiratory chain complex assembly

The aggregation, arrangement and bonding together of a set of components to form a mitochondrial respiratory chain complex.


cardiac muscle cell apoptotic process

A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a cardiac muscle cell and result in its death. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.


regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion

Any process that modulates the frequency, rate or extent of cardiac muscle contraction via the regulation of the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol. The sarcoplasmic reticulum is the endoplasmic reticulum of striated muscle, specialised for the sequestration of calcium ions that are released upon receipt of a signal relayed by the T tubules from the neuromuscular junction.


monoamine transport

The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.


scaffold protein binding

Binding to a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.


regulation of heart rate by cardiac conduction

A cardiac conduction process that modulates the frequency or rate of heart contraction.


endocardial cushion to mesenchymal transition involved in heart valve formation

A transition where an endocardial cushion cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell that will contribute to the formation of a cardiac valve.


embryonic heart tube anterior/posterior pattern specification

The establishment, maintenance and elaboration of cell differentiation that results in the anterior/posterior subdivision of the embryonic heart tube. In Drosophila this results in subdivision of the dorsal vessel into to the posterior heart proper and the anterior aorta.


malate-aspartate shuttle

The process of transferring reducing equivalents from the cytosol into the mitochondria; NADH is used to synthesise malate in the cytosol; this compound is then transported into the mitochondria where it is converted to oxaloacetate using NADH, the oxaloacetate reacts with gluamate to form aspartate, and the aspartate then returns to the cytosol to complete the cycle.


negative regulation of mitochondrial electron transport, NADH to ubiquinone

Any process that stops, prevents or reduces the frequency, rate or extent of mitochondrial electron transport, NADH to ubiquinone.


negative regulation of smooth muscle cell apoptotic process

Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process.


desensitization of G protein-coupled receptor signaling pathway

The process that stops, prevents, or reduces the frequency, rate or extent of G protein-coupled receptor signaling pathway after prolonged stimulation with an agonist of the pathway.


glycolytic process from galactose

The chemical reactions and pathways resulting in the breakdown of galactose into pyruvate, with the concomitant production of a small amount of ATP.


regulation of cardiac muscle cell membrane potential

Any process that modulates the establishment or extent of a membrane potential in a cardiac muscle cell (a cardiomyocyte). A membrane potential is the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.


cardiac muscle cell fate commitment

The commitment of cells to specific cardiac muscle cell fates and their capacity to differentiate into cardiac muscle cells. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.


beta2-adrenergic receptor activity

Combining with epinephrine or norepinephrine to initiate a change in cell activity via activation of a G protein, with pharmacological characteristics of beta2-adrenergic receptors.


beta1-adrenergic receptor activity

Combining with epinephrine or norepinephrine to initiate a change in cell activity via activation of a G protein, with pharmacological characteristics of beta1-adrenergic receptors.


negative regulation of cytosolic calcium ion concentration

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


atrioventricular bundle cell differentiation

The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell of the atrioventricular bundle. These cells are specialized cardiomyocytes that transmit signals from the AV node to the cardiac Purkinje fibers.


lymph vessel development

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


cardiac muscle tissue development

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


coronary vasculature development

The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.


ventricular cardiac muscle tissue development

The process whose specific outcome is the progression of ventricular cardiac muscle over time, from its formation to the mature structure.


cardiac chamber development

The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart.


atrial septum development

The progression of the atrial septum over time, from its initial formation to the mature structure.


adult heart development

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


sinoatrial node cell development

The process whose specific outcome is the progression of a sinoatrial (SA) node cell over time, from its formation to the mature state. SA node cells are pacemaker cells that are found in the sinoatrial node.


caveolar macromolecular signaling complex

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A complex composed of proteins required for beta adrenergic receptor activation of protein kinase A. It includes the Cav 12. subunit of L-type calcium channel, protein kinase A regulatory subunit 2(PKAR2), adenyl cyclase, beta-adrenergic receptor, G-alpha-S, protein phosphatase 2A (PP2A) and caveolin 3 (CAV3).


F-actin-capping protein subunit beta isoform 1 (mouse)

An F-actin-capping protein subunit beta isoform 1 that is encoded in the genome of mouse.


FH1/FH2 domain-containing protein 3 isoform FHOS2L (mouse)

An FH1/FH2 domain-containing protein 3 isoform FHOS2L that is encoded in the genome of mouse.


Q2VEB3_MOUSE A-kinase anchoring protein beta (trembl)

An A-kinase anchor protein 6 (mouse) that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:Q2VEB3.


endocardium formation

Formation of the endocardium of the heart. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.


embryonic heart tube formation

The process that gives rise to the embryonic heart tube. This process pertains to the initial formation of a structure from unspecified parts. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.


cardiac right ventricle formation

The developmental process pertaining to the initial formation of a right cardiac ventricle from unspecified parts.


memory

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


cell death

Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).


adult behavior

Behavior in a fully developed and mature organism.


extrathymic T cell selection

The process of T cell selection that occurs in extrathymic locations, often resulting T cells of distinct specificities from those selected in the thymus.


gamma-delta intraepithelial T cell

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A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses.


digestive tract epithelium

biolink:GrossAnatomicalStructure biolink:AnatomicalEntity biolink:OrganismalEntity biolink:BiologicalEntity biolink:NamedThing biolink:PhysicalEssence biolink:SubjectOfInvestigation biolink:ThingWithTaxon biolink:PhysicalEssenceOrOccurrent

An epithelium that lines the lumen of the digestive tract.


BTNL3_HUMAN Butyrophilin-like protein 3 (sprot)

A butyrophilin-like protein 3 that is encoded in the genome of human.


BTNL8_HUMAN Butyrophilin-like protein 8 (sprot)

A butyrophilin-like protein 8 that is encoded in the genome of human.


mRNA methylation

The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.


mRNA splicing, via spliceosome

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.


pole plasm mRNA localization

Any process in which mRNA is transported to, or maintained in, the oocyte pole plasm. An example of this is found in Drosophila melanogaster.


mitochondrial translational initiation

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


negative regulation of cytoplasmic translation

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


electron transport coupled proton transport

The transport of protons against an electrochemical gradient, using energy from electron transport.


eyeball of camera-type eye

The core globe-shaped component of the camera-type eye.


ELAV-like protein 4 isoform m9 (mouse)

An ELAV-like protein 4 (mouse) that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:Q61701-10.


ELAV-like protein 4 isoform m5 (mouse)

An ELAV-like protein 4 (mouse) that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:Q61701-6.


ELAV-like protein 4 isoform m3 (mouse)

An ELAV-like protein 4 (mouse) that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:Q61701-4.


ELAV-like protein 4 isoform m1 (mouse)

An ELAV-like protein 4 (mouse) that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:Q61701-1.


tissue migration

The process in which the population of cells that make up a tissue undergo directed movement.


smooth muscle cell proliferation

The multiplication or reproduction of smooth muscle cells, resulting in the expansion of a cell population.


reactive gliosis

A neuroinflammatory response, occurring over several days, during which glial cells undergo nonspecific reactive changes in response to damage to the central nervous system (CNS); typically involves the proliferation or hypertrophy of different types of glial cells.


microglial cell activation

The change in morphology and behavior of a microglial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.


KH domain-containing RNA-binding protein QKI isoform 6 (mouse)

A KH domain-containing RNA-binding protein QKI (mouse) that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:Q9QYS9-6.


type II interferon-mediated signaling pathway

The series of molecular signals initiated by interferon-gamma binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.


receptor-mediated endocytosis

An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.


mRNA 3'-end processing

Any process involved in forming the mature 3' end of an mRNA molecule.


proton transmembrane transport

The directed movement of a proton across a membrane.


sperm-egg recognition

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


granulocyte differentiation

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.


miRNA metabolic process

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.


cellular response to xenobiotic stimulus

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


telomere maintenance

Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.


renal water homeostasis

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


toll-like receptor signaling pathway

The series of molecular signals initiated by a ligand binding to a toll-like receptor of a target cell. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate an innate immune response.


protein targeting to mitochondrion

The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.


rRNA processing

Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.


cristae formation

The assembly of cristae, the inwards folds of the inner mitochondrial membrane.


error-prone translesion synthesis

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.


cellular response to steroid hormone stimulus

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


The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.


adherens junction organization

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell-cell junction composed of the epithelial cadherin-catenin complex at which the cytoplasmic face of the plasma membrane is attached to actin filaments.


positive regulation of BMP signaling pathway

Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity.


cobalamin metabolic process

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


cobalamin transport

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.


DNA methylation on cytosine

The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule.


cell redox homeostasis

Any process that maintains the redox environment of a cell or compartment within a cell.


mRNA export from nucleus

The directed movement of mRNA from the nucleus to the cytoplasm.


oxygen transport

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.


lipid transport

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.


The series of molecular signals initiated by interleukin-18 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


mitochondrial electron transport, succinate to ubiquinone

The transfer of electrons from succinate to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex II.


regulation of immune response

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


tRNA modification

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.


anaphase-promoting complex-dependent catabolic process

The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.


positive regulation of protein export from nucleus

Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.


lactose biosynthetic process

The chemical reactions and pathways resulting in the formation of lactose, the disaccharide galactopyranosyl-glucose.


mitochondrial translational elongation

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


hyaluronan catabolic process

The chemical reactions and pathways resulting in the breakdown of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.


retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum

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.


ciliary basal body-plasma membrane docking

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.


translational elongation

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


heparan sulfate proteoglycan catabolic process

The chemical reactions and pathways resulting in the breakdown of proteoglycan containing heparan sulfate, any member of a group of glycosaminoglycans that have repeat units consisting of alternating alpha-(1->4) linked hexuronic acid and glucosamine residues, the former being a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids, and the latter being either sulfated or acetylated on its amino group as well as sulfated on one of its hydroxyl groups.


base-excision repair

In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.


termination of RNA polymerase II transcription

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


nuclear export

The directed movement of substances out of the nucleus.


suppression by symbiont of host apoptotic process

Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of programmed cell death in the host, where programmed cell death proceeds by apoptosis. The host is defined as the larger of the organisms involved in a symbiotic interaction.


apoptotic DNA fragmentation

The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.


tRNA catabolic process

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.


bile acid and bile salt transport

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.


low-density lipoprotein particle clearance

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


regulation of cellular amino acid metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids.


cellular response to glucagon stimulus

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


telomere capping

A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.


sterol metabolic process

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


retinoid metabolic process

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.


post-translational protein modification

The process of covalently altering one or more amino acids in a protein after the protein has been completely translated and released from the ribosome.


transmembrane transport

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


regulation of type I interferon-mediated signaling pathway

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


DNA double-strand break processing

The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang.


regulation of glycolytic process

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


negative regulation of transcription initiation by RNA polymerase II

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


DNA replication initiation

The process in which DNA-dependent DNA replication is started; it begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, followed by DNA unwinding.


toll-like receptor 9 signaling pathway

The series of molecular signals initiated by a ligand binding to the endolysosomal toll-like receptor 9.


positive regulation of epidermal growth factor receptor signaling pathway

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


peptidyl-glutamic acid carboxylation

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


toll-like receptor 3 signaling pathway

The series of molecular signals initiated by a ligand binding to the endolysosomal toll-like receptor 3.


biotin metabolic process

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.


molybdopterin cofactor biosynthetic process

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.


negative regulation of G2/M transition of mitotic cell cycle

Any signaling pathway that decreases or inhibits the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.


positive regulation of ceramide biosynthetic process

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


neurotrophin TRK receptor signaling pathway

The series of molecular signals initiated by neurotrophin binding to its receptor on the surface of a target cell where the receptor possesses tyrosine kinase activity, and ending with the regulation of a downstream cellular process, e.g. transcription.


L-ascorbic acid metabolic process

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.


T cell costimulation

The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.


positive regulation of tyrosine phosphorylation of STAT protein

Any process that activates or increases the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a STAT (Signal Transducer and Activator of Transcription) protein.


mismatch repair

A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.


transcription by RNA polymerase III

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


low-density lipoprotein particle remodeling

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.


paraxial mesoderm formation

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


bicellular tight junction assembly

The aggregation, arrangement and bonding together of a set of components to form a tight junction, an occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet.


nuclear-transcribed mRNA poly(A) tail shortening

Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.


binding of sperm to zona pellucida

The process in which the sperm binds to the zona pellucida glycoprotein layer of the egg. The process begins with the attachment of the sperm plasma membrane to the zona pellucida and includes attachment of the acrosome inner membrane to the zona pellucida after the acrosomal reaction takes place.


negative regulation of signal transduction

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


activation of adenylate cyclase activity

Any process that initiates the activity of the inactive enzyme adenylate cyclase.


positive regulation of extrinsic apoptotic signaling pathway in absence of ligand

Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.


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

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.


positive regulation of non-membrane spanning protein tyrosine kinase activity

Any process that activates or increases the frequency, rate or extent of non-membrane spanning protein tyrosine kinase activity.


heme biosynthetic process

The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.


termination of RNA polymerase I transcription

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.


regulation of glucose transmembrane transport

Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.


adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway

A G protein-coupled receptor signaling pathway in which the signal is transmitted via the inhibition of adenylyl cyclase activity and a subsequent decrease in the intracellular concentration of cyclic AMP (cAMP).


mitotic prophase

The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell.


nucleotide-excision repair, preincision complex assembly

The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.


autophagosome maturation

Removal of PI3P and Atg8/LC3 after the closure of the phagophore and before the fusion with the endosome/lysosome (e.g. mammals and insects) or vacuole (yeast), and that very likely destabilizes other Atg proteins and thus enables their efficient dissociation and recycling.


transferrin transport

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


mitochondrial respiratory chain complex I assembly

The aggregation, arrangement and bonding together of a set of components to form mitochondrial respiratory chain complex I.


DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest

A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.


sensory perception of taste

The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process.


negative regulation of axonogenesis

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


regulation of bicellular tight junction assembly

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


acyl-CoA metabolic process

The chemical reactions and pathways involving acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with an acyl group.


positive regulation of Ras protein signal transduction

Any process that activates or increases the frequency, rate or extent of Ras protein signal transduction.


regulation of generation of precursor metabolites and energy

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.


bicarbonate transport

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


regulation of type II interferon-mediated signaling pathway

Any process that modulates the rate, frequency or extent of an interferon-gamma-mediated signaling pathway.


regulation of cysteine-type endopeptidase activity involved in apoptotic process

Any process that modulates the activity of a cysteine-type endopeptidase involved in apoptosis.


axial mesoderm formation

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


regulation of cell motility

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


regulation of androgen receptor signaling pathway

Any process that modulates the rate, frequency, or extent of the androgen receptor signaling pathway.


activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c

Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process and is mediated by cytochrome c.


long-chain fatty acid transport

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 is a fatty acid with an aliphatic tail of 13 to 21 carbons.


keratinization

The process in which the cytoplasm of the outermost cells of the vertebrate epidermis is replaced by keratin. Keratinization occurs in the stratum corneum, feathers, hair, claws, nails, hooves, and horns.


positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway

Any process that activates or increases the frequency, rate or extent of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway.


regulation of regulatory T cell differentiation

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


neurotransmitter transport

The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.


regulation of hematopoietic stem cell differentiation

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


post-Golgi vesicle-mediated transport

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.


fusion of sperm to egg plasma membrane involved in single fertilization

The binding and fusion of a sperm, with the plasma membrane of the oocyte as part of the process of single fertilization. In sperm with flagella, binding occurs at the posterior (post-acrosomal) region of the sperm head.


complement activation, lectin pathway

Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.


DNA ligation

The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.


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.


negative regulation of neurotrophin TRK receptor signaling pathway

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


regulation of acetyl-CoA biosynthetic process from pyruvate

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate.


vitamin E metabolic process

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.


phosphatidylinositol-mediated signaling

The series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.


RNA export from nucleus

The directed movement of RNA from the nucleus to the cytoplasm.


regulation of transcription involved in G1/S transition of mitotic cell cycle

Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.


base-excision repair, gap-filling

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.


positive regulation of transcription of Notch receptor target

The activation of transcription of specific genes as a result of Notch signaling, mediated by the Notch intracellular domain.


regulation of miRNA-mediated gene silencing

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


CENP-A containing chromatin assembly

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.


phospholipid transport

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.


7-methylguanosine mRNA capping

Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.


fatty acid catabolic process

The chemical reactions and pathways resulting in the breakdown of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.


negative regulation of DNA recombination at telomere

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


chylomicron remnant clearance

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


chylomicron assembly

The non-covalent aggregation and arrangement of proteins and lipids in the intestine to form a chylomicron.


very-low-density lipoprotein particle assembly

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


regulation of rhodopsin mediated signaling pathway

Any process that modulates the frequency, rate or extent of rhodopsin-mediated signaling.


regulatory ncRNA-mediated post-transcriptional gene silencing

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


siRNA processing

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.


regulation of keratinocyte differentiation

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


carboxylic acid metabolic process

The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).


protein N-linked glycosylation via asparagine

The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification.


positive regulation of neurotrophin TRK receptor signaling pathway

Any process that activates or increases the frequency, rate or extent of the neurotrophin TRK receptor signaling pathway.


vitamin D metabolic process

The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).


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.


response to metal ion

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.


transcription initiation at mitochondrial promoter

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


positive regulation of phospholipase C activity

Any process that increases the rate of phospholipase C activity.


glucocorticoid biosynthetic process

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


C21-steroid hormone biosynthetic process

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


folic acid metabolic process

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.


gap junction assembly

Assembly of gap junctions, which are found in most animal tissues, and serve as direct connections between the cytoplasms of adjacent cells. They provide open channels through the plasma membrane, allowing ions and small molecules (less than approximately a thousand daltons) to diffuse freely between neighboring cells, but preventing the passage of proteins and nucleic acids.


positive regulation of receptor signaling pathway via STAT

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


regulation of megakaryocyte differentiation

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


DNA dealkylation involved in DNA repair

The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).


death-inducing signaling complex assembly

A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a death domain (DD) interaction, as part of the extrinsic apoptotic signaling pathway.


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

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


depyrimidination

The disruption of the bond between the sugar in the backbone and the C or T base, causing the base to be removed and leaving a depyrimidinated sugar.


depurination

The disruption of the bond between the sugar in the backbone and the A or G base, causing the base to be removed and leaving a depurinated sugar.


base-excision repair, DNA ligation

The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair.


histone mRNA metabolic process

The chemical reactions and pathways involving an mRNA encoding a histone.


ERBB2 signaling pathway

The series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB2 on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.


intracellular transport of virus

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


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

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.


vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane

The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane of the ERGIC. This can involve anterograde or retrograde transport vesicles.


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.


negative regulation of blood coagulation, extrinsic pathway

Any process that stops, prevents or reduces the frequency, rate or extent of blood coagulation, extrinsic pathway.


negative regulation of blood coagulation, intrinsic pathway

Any process that stops, prevents or reduces the frequency, rate or extent of blood coagulation, intrinsic pathway.


inositol phosphate metabolic process

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


C-terminal protein lipidation

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


sulfur amino acid catabolic process

The chemical reactions and pathways resulting in the breakdown of amino acids containing sulfur, comprising cysteine, methionine and selenocysteine.


sulfur amino acid metabolic process

The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine.


termination of mitochondrial transcription

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


activation of protein kinase A activity

Any process that initiates the activity of the inactive enzyme protein kinase A.


positive regulation of cellular metabolic process

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


negative regulation of MyD88-independent toll-like receptor signaling pathway

Any process that stops, prevents, or reduces the frequency, rate, or extent of MyD88-independent toll-like receptor signaling pathway.


activation of phospholipase C activity

The initiation of the activity of the inactive enzyme phospolipase C as the result of The series of molecular signals generated as a consequence of a G protein-coupled receptor binding to its physiological ligand.


toll-like receptor 10 signaling pathway

The series of molecular signals initiated by a ligand binding to toll-like receptor 10.


toll-like receptor TLR1:TLR2 signaling pathway

The series of molecular signals initiated by a ligand binding of a heterodimeric TLR1:TLR2 complex, followed by transmission of the signal by the activated receptor, and ending with the regulation of a downstream cellular process, e.g. transcription.


telomere maintenance via semi-conservative replication

The process in which telomeric DNA is synthesized semi-conservatively by the conventional replication machinery and telomeric accessory factors as part of cell cycle DNA replication.


regulation of anaphase-promoting complex-dependent catabolic process

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


negative regulation of ERBB signaling pathway

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


negative regulation of platelet-derived growth factor receptor-beta signaling pathway

Any process that stops, prevents or reduces the frequency, rate or extent of platelet-derived growth factor receptor-beta signaling pathway.


import into nucleus

The directed movement of substances into the nucleus.


spliceosomal snRNP assembly

The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome.


beta-catenin destruction complex assembly

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


carnitine shuttle

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.


sequestering of BMP from receptor via BMP binding

Binding to a bone morphogenetic protein (BMP) in the extracellular region, and inhibiting BMP signaling by preventing BMP from binding to its cell surface receptor.


regulation of transcription initiation by RNA polymerase II

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


ferredoxin metabolic process

The chemical reactions and pathways involving ferredoxin, any simple, nonenzymatic iron-sulfur protein that is characterized by having equal numbers of atoms of iron and labile sulfur. Iron and sulfur atoms are present in one or two clusters of two or four atoms of each.


selenocysteine metabolic process

The chemical reactions and pathways involving selenocysteine, an essential component of glutathione peroxidase and some other proteins.


Fc-epsilon receptor signaling pathway

The series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.


regulation of extrinsic apoptotic signaling pathway via death domain receptors

Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.


negative regulation of netrin-activated signaling pathway

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


chaperone mediated protein folding independent of cofactor

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.


post-chaperonin tubulin folding pathway

Completion of folding of alpha- and beta-tubulin; takes place subsequent to chaperonin-mediated partial folding; mediated by a complex of folding cofactors.


muscle filament sliding

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.


exonucleolytic catabolism of deadenylated mRNA

The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail.


hemidesmosome assembly

Assembly of hemidesmosomes, integrin-containing protein complexes that bind to laminin in the basal lamina. Hemidesmosomes form the contact between the basal surface of epithelial cells and the underlying basal lamina.


mitochondrial translational termination

The process resulting in the release of a polypeptide chain from the ribosome in a mitochondrion, usually in response to a termination codon (note that mitochondria use variants of the universal genetic code that differ between different taxa).


aflatoxin metabolic process

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.


piRNA processing

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.


intraciliary transport involved in cilium assembly

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


DNA synthesis involved in DNA repair

Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.


strand displacement

The rejection of the broken 3' single-strand DNA molecule that formed heteroduplex DNA with its complement in an intact duplex DNA. The Watson-Crick base pairing in the original duplex is restored. The rejected 3' single-strand DNA molecule reanneals with its original complement to reform two intact duplex molecules.


nucleotide-excision repair, DNA damage recognition

The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix.


nucleotide-excision repair, DNA gap filling

Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.


nucleotide-excision repair, preincision complex stabilization

The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.


nucleotide-excision repair, DNA duplex unwinding

The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.


glycine catabolic process

The chemical reactions and pathways resulting in the breakdown of glycine, aminoethanoic acid.


negative regulation of cellular amino acid metabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid.


positive regulation of amino acid metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid.


purine ribonucleoside monophosphate biosynthetic process

The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar.


regulation of cell cycle G2/M phase transition

Any signaling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.


SCF complex assembly

The aggregation, arrangement and bonding together of a set of components to form the SKP1-Cullin/Cdc53-F-box protein ubiquitin ligase (SCF) complex.


low-density lipoprotein particle receptor catabolic process

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.


digestion

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


regulation of cytokine-mediated signaling pathway

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


regulation of B cell receptor signaling pathway

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.


protein side chain deglutamylation

The removal of a glutamate residue from the side chain of a protein. Glutamate side chains are added to glutamic acid residues within the primary protein sequence during polyglutamylation.


protein polyglycylation

The addition of glycyl units covalently bound to the gamma carboxyl group peptidyl-glutamic acid.


C-terminal protein amino acid modification

The alteration of the C-terminal amino acid residue in a protein.


chylomicron remodeling

The acquisition, loss or modification of a protein or lipid within a chylomicron, including the hydrolysis of triglyceride by lipoprotein lipase and the subsequent loss of free fatty acid.


high-density lipoprotein particle clearance

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


very-low-density lipoprotein particle clearance

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


high-density lipoprotein particle remodeling

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.


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.


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.


negative regulation of primary miRNA processing

Any process that stops, prevents or reduces the frequency, rate or extent of primary microRNA processing.


trimming of first mannose on A branch

The removal of the first alpha-1,2-linked mannose from the A-chain of a glycoprotein oligosaccharide in the endoplasmic reticulum.


trimming of terminal mannose on B branch

The removal of an alpha-1,2-linked mannose from the B-chain of a glycoprotein oligosaccharide in the endoplasmic reticulum.


mannose trimming involved in glycoprotein ERAD pathway

The removal of one or more alpha 1,2-linked mannose residues from a mannosylated protein that occurs as part of glycoprotein ER-associated glycoprotein degradation (gpERAD).


trimming of second mannose on A branch

The removal of the second alpha-1,2-linked mannose from the A-chain of a glycoprotein oligosaccharide in the endoplasmic reticulum.


trimming of terminal mannose on C branch

The removal of an alpha-1,2-linked mannose from the C-chain of a glycoprotein oligosaccharide in the endoplasmic reticulum.


endoplasmic reticulum mannose trimming

Any protein alpha-1,2-demannosylation that takes place in the endoplasmic reticulum quality control compartment (ERQC).


Notch receptor processing, ligand-dependent

The proteolytic cleavages to the Notch protein that occur as a result of ligand binding. Ligand binding at the cell surface exposes an otherwise inaccessible cleavage site in the extracellular portion of Notch, which when cleaved releases a membrane-tethered form of the Notch intracellular domain. Subsequent cleavage within the transmembrane domain then leads to the release of the soluble Notch intracellular domain (NICD).


The series of molecular signals initiated by interleukin-21 binding to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


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.


protein import into peroxisome membrane

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.


protein insertion into ER membrane

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.


late endosomal microautophagy

The autophagy process by which cytosolic proteins targeted for degradation are tagged with a chaperone and are directly transferred into and degraded in a late endosomal compartment.


regulation of heme oxygenase activity

Any process that modulates the frequency, or rate of heme oxygenase activity.


lateral mesoderm formation

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


growth hormone receptor signaling pathway via JAK-STAT

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.


TFAM_HUMAN Transcription factor A, mitochondrial (sprot)

A transcription factor A, mitochondrial that is encoded in the genome of human.


phosphatidylinositol 3-phosphate

A phosphatidylinositol monophosphate carrying the phosphate group at the 3-position.


NDST1_HUMAN Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (sprot)

A bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 that is encoded in the genome of human.


Fumarate

A C4-dicarboxylate that is the E-isomer of but-2-enedioate(2-)


L-malate

An optically active form of malate having (S)-configuration.


Oxalacetate

A C4-dicarboxylate resuting from deprotonation of both carboxy groups of oxaloacetic acid.


SOCS1_HUMAN Suppressor of cytokine signaling 1 (sprot)

A suppressor of cytokine signaling 1 that is encoded in the genome of human.


Adenosine

A ribonucleoside composed of a molecule of adenine attached to a ribofuranose moiety via a beta-N(9)-glycosidic bond.


A purine 2'-deoxyribonucleoside having guanine as the nucleobase.


Guanosine

A purine nucleoside in which guanine is attached to ribofuranose via a beta-N(9)-glycosidic bond.


Inosine

A purine nucleoside in which hypoxanthine is attached to ribofuranose via a beta-N(9)-glycosidic bond.


A purine 2'-deoxyribonucleoside that is inosine in which the hydroxy group at position 2' is replaced by a hydrogen.


Dihydrothymine

A pyrimidone obtained by formal addition of hydrogen across the 5,6-position of thymine.


Dihydrouracil

A pyrimidine obtained by formal addition of hydrogen across the 5,6-position of uracil.


Uracil

A common and naturally occurring pyrimidine nucleobase in which the pyrimidine ring is substituted with two oxo groups at positions 2 and 4. Found in RNA, it base pairs with adenine and replaces thymine during DNA transcription.


Hydroxyprogesterone

A 17alpha-hydroxy steroid that is the 17alpha-hydroxy derivative of progesterone.


Cortodoxone

A deoxycortisol that is cortisol in which the hydroxy group at position 11 has been replaced by a hydrogen.


ceramide

Ceramides (N-acyl-sphingoid bases) are a major subclass of sphingoid base derivatives with an amide-linked fatty acid. The fatty acids are typically saturated or monounsaturated with chain lengths from 14 to 26 carbon atoms; the presence of a hydroxyl group on carbon 2 is fairly common. Ceramides are generally precursors of more complex sphingolipids. In the illustrated generalised structure, R(1) = OH, OX (where X = acyl, glycosyl, phosphate, phosphonate, etc.), or H.


STX17_HUMAN Syntaxin-17 (sprot)

A syntaxin-17 that is encoded in the genome of human.


Hypoxanthine

A purine nucleobase that consists of purine bearing an oxo substituent at position 6.


Deoxyadenosine-phosphate

A 2'-deoxyribonucleoside 5'-monophosphate(2-) obtained by deprotonation of the phosphate OH groups of 2'-deoxyadenosine 5'-monophosphate (dAMP).


dGMP dianion

A 2'-deoxyribonucleoside 5'-monophosphate(2-) obtained by deprotonation of the phosphate OH groups of 2'-deoxyguanosine 5'-monophosphate (dGMP).


Dianion of N-phosphocreatine arising from deprotonation of the phospho and carboxy groups and protonation of the guanidino group; major species at pH 7.3.


Zwitterionic form of creatine arising from transfer of a proton from the carboxy to the guanidino group; major species at pH 7.3.


DDIT3_HUMAN DNA damage-inducible transcript 3 protein (sprot)

A DNA damage-inducible transcript 3 protein that is encoded in the genome of human.


2'-Deoxyinosine 5'-phosphate(2-)

A 2'-deoxyribonucleoside 5'-monophosphate(2-) obtained by deprotonation of the phosphate OH groups of 2'-deoxyinosine 5'-monophosphate; major species at pH 7.3.


A 2'-deoxyribonucleoside 5'-triphosphate(4-) resulting from deprotonation of the triphosphate OH groups of 2'-deoxyuridine-5'-triphosphate (dUTP); major species at pH 7.3.


Uridine-diphosphate

A nucleoside 5'-diphosphate(3-) arising from deprotonation of the diphosphate OH groups of uridine 5'-diphosphate (UDP); major species at pH 7.3.


dUDP trianion

A 2'-deoxyribonucleoside 5'-diphosphate obtained by deprotonation of the diphosphate OH groups of 2'-deoxyuridine 5'-diphosphate (dUDP).


An L-alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of L-tryptophan; major species at pH 7.3.


SYUA_HUMAN Alpha-synuclein (sprot)

An alpha-synuclein that is encoded in the genome of human.


LPIN1_HUMAN Phosphatidate phosphatase LPIN1 (sprot)

A phosphatidate phosphatase LPIN1 that is encoded in the genome of human.


HDAC3_HUMAN Histone deacetylase 3 (sprot)

A histone deacetylase 3 that is encoded in the genome of human.


UIMC1_HUMAN BRCA1-A complex subunit RAP80 (sprot)

A BRCA1-A complex subunit RAP80 that is encoded in the genome of human.


FZR1_HUMAN Fizzy-related protein homolog (sprot)

A fizzy-related protein that is encoded in the genome of human.


CDK4_HUMAN Cyclin-dependent kinase 4 (sprot)

A cell division protein kinase 4 that is encoded in the genome of human.


CDK6_HUMAN Cyclin-dependent kinase 6 (sprot)

A cyclin-dependent kinase 6 that is encoded in the genome of human.


NEDD8 ultimate buster 1 isoform h2 (human)

A NEDD8 ultimate buster 1 (human) that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:Q9Y5A7-2.


(R)-mevalonate

The (R)-enantiomer of mevalonate.


A 3-oxo-5alpha- steroid that is zymosterol which has been substituted by a methyl group at C-4, and in which the 3-hydroxy function has been oxidised to an oxo group.


A 3beta-sterol formed formally by loss of a methyl group from the 14-position of lanosterol.


3-hydroxy-3-methylglutaryl-coenzyme A

An acyl-CoA oxoanion that results from the removal of all five protons from the phosphate and carboxylic acid groups of (3S)-3-hydroxy-3-methylglutaryl-CoA.


A 2,3-epoxysqualene in which the chiral centre has S configuration. It is converted into lanosterol by lanosterol synthase (EC 5.4.99.7) in a key rate-limiting step in the biosynthesis of chloesterol, steroid hormones, and vitamin D.


Lanosterol

A tetracyclic triterpenoid that is lanosta-8,24-diene substituted by a beta-hydroxy group at the 3beta position. It is the compound from which all steroids are derived.


Squalene

A triterpene consisting of 2,6,10,15,19,23-hexamethyltetracosane having six double bonds at the 2-, 6-, 10-, 14-, 18- and 22-positions with (all-E)-configuration.


Trianion of (R)-5-phosphomevalonic acid arising from deprotonation of the carboxy and phosphate OH groups; major species at pH 7.3.


A 3-oxoacyl-CoA(4-) arising from deprotonation of the phosphate and diphosphate OH groups of acetoacetyl-CoA.


ABCD4_HUMAN Lysosomal cobalamin transporter ABCD4 (sprot)

A lysosomal cobalamin transporter ABCD4 that is encoded in the genome of human.


EREG_HUMAN Proepiregulin (sprot)

A proepiregulin that is encoded in the genome of human.


G6PT1_HUMAN Glucose-6-phosphate exchanger SLC37A4 (sprot)

A glucose-6-phosphate exchanger SLC37A4 that is encoded in the genome of human.


CUBN_HUMAN Cubilin (sprot)

A cubilin that is encoded in the genome of human.


alpha-D-GALACTOSE

D-Galactopyranose having alpha-configuration at the anomeric centre.


5-Phosphoribosyl 1-pyrophosphate

Pentaanion of 5-O-phosphono-alpha-D-ribofuranosyl diphosphate arising from deprotonation of the phosphate and diphosphate OH groups; major species at pH 7.3.


Deoxyadenosine-triphosphate

A 2'-deoxyribonucleoside 5'-triphosphate(4-) that is the tetraanion of 2'-deoxyadenosine 5'-triphosphate (dATP), arising from deprotonation of the four triphosphate OH groups; major species at pH 7.3.


2-Amino-5-guanidinovaleric acid

The L-enantiomer of argininium(1+).


ZDHC9_HUMAN Palmitoyltransferase ZDHHC9 (sprot)

A palmitoyltransferase ZDHHC9 that is encoded in the genome of human.


CHST7_HUMAN Carbohydrate sulfotransferase 7 (sprot)

A carbohydrate sulfotransferase 7 that is encoded in the genome of human.


An NDP-alpha-D-glucose(2-) arising from deprotonation of the diphosphate OH groups of UDP-D-glucose; major species at pH 7.3.


UDP-N-acetyl-alpha-D-glucosamine

Dianion of UDP-N-acetyl-alpha-D-glucosamine arising from deprotonation of both free diphosphate OH groups; major species at pH 7.3.


HS3S5_HUMAN Heparan sulfate glucosamine 3-O-sulfotransferase 5 (sprot)

A heparan sulfate glucosamine 3-O-sulfotransferase 5 that is encoded in the genome of human.


B4GT1_HUMAN Beta-1,4-galactosyltransferase 1 (sprot)

A beta-1,4-galactosyltransferase 1 that is encoded in the genome of human.


B3GN7_HUMAN UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7 (sprot)

A UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7 that is encoded in the genome of human.


B4GA1_HUMAN Beta-1,4-glucuronyltransferase 1 (sprot)

A beta-1,4-glucuronyltransferase 1 that is encoded in the genome of human.


B3GN3_HUMAN N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 3 (sprot)

An N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 3 that is encoded in the genome of human.


B3GN4_HUMAN N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 4 (sprot)

An N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 4 that is encoded in the genome of human.


B3GN2_HUMAN N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 (sprot)

An N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 that is encoded in the genome of human.


CHST1_HUMAN Carbohydrate sulfotransferase 1 (sprot)

A carbohydrate sulfotransferase 1 that is encoded in the genome of human.


CHD1L_HUMAN Chromodomain-helicase-DNA-binding protein 1-like (sprot)

A chromodomain-helicase-DNA-binding protein 1-like that is encoded in the genome of human.


DLG4_HUMAN Disks large homolog 4 (sprot)

A disks large homolog 4 that is encoded in the genome of human.


glycine zwitterion

An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of glycine.


fatty acid anion

The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid.


An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of 5-hydroxy-L-tryptophan; major species at pH 7.3.


MUC2_HUMAN Mucin-2 (sprot)

A mucin-2 that is encoded in the genome of human.


TPSN_HUMAN Tapasin (sprot)

A tapasin that is encoded in the genome of human.


Chenodeoxycholate anion

Conjugate base of chenodeoxycholic acid; major species at pH 7.3.


Ascorbate

The L-enantiomer of ascorbate and conjugate base of L-ascorbic acid, arising from selective deprotonation of the 3-hydroxy group. Required for a range of essential metabolic reactions in all animals and plants.


A  purine ribonucleoside 5'-diphosphate resulting from the formal condensation of the hydroxy group at the 5' position of guanosine with pyrophosphoric acid.


MUC5B_HUMAN Mucin-5B (sprot)

A mucin-5B that is encoded in the genome of human.


VWF_HUMAN von Willebrand factor (sprot)

A von Willebrand factor that is encoded in the genome of human.


GBP2_HUMAN Guanylate-binding protein 2 (sprot)

A guanylate-binding protein 2 that is encoded in the genome of human.


GBP5_HUMAN Guanylate-binding protein 5 (sprot)

A guanylate-binding protein 5 that is encoded in the genome of human.


Sulfate

A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid.


alpha-aminoacyl-tRNA

Any ribonucleic acid that is transfer RNA in which one or more of the free OH groups carries an alpha-aminoacyl group.


TRNT1_HUMAN CCA tRNA nucleotidyltransferase 1, mitochondrial (sprot)

A CCA tRNA nucleotidyltransferase 1, mitochondrial that is encoded in the genome of human.


An organic anion that is the conjugate base of riboflavin resulting from the removal of a proton from the nitrogen at position 3 (between the two carbonyl groups). Major microspecies at pH 7.3.


Trianion of flavin adenine dinucleotide arising from deprotonation of the diphosphate OH groups and the imide nitrogen.


A16L1_HUMAN Autophagy-related protein 16-1 (sprot)

An autophagy-related protein 16-1 that is encoded in the genome of human.


The conjugate base of a 1-phosphatidyl-1D-myo-inositol; major species at pH 7.3.


ATG10_HUMAN Ubiquitin-like-conjugating enzyme ATG10 (sprot)

A ubiquitin-like-conjugating enzyme ATG10 that is encoded in the genome of human.


ATG12_HUMAN Ubiquitin-like protein ATG12 (sprot)

A ubiquitin-like protein ATG12 that is encoded in the genome of human.


ATG5_HUMAN Autophagy protein 5 (sprot)

An autophagy protein 5 that is encoded in the genome of human.


HLAA_HUMAN HLA class I histocompatibility antigen, A alpha chain (sprot)

An MHC class I histocompatibility antigen A alpha chain that is encoded in the genome of human.


PDIA3_HUMAN Protein disulfide-isomerase A3 (sprot)

A protein disulfide-isomerase A3 that is encoded in the genome of human.


ERAP1_HUMAN Endoplasmic reticulum aminopeptidase 1 (sprot)

An endoplasmic reticulum aminopeptidase 1 that is encoded in the genome of human.


CALR_HUMAN Calreticulin (sprot)

A calreticulin that is encoded in the genome of human.


B2MG_HUMAN Beta-2-microglobulin (sprot)

A beta-2-microglobulin that is encoded in the genome of human.


Pyridoxal 5'-phosphate(2-)

The dianion resulting from the removal of two protons from the phosphate group of pyridoxal 5'-phosphate.


Biotin

An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.


HDAC2_HUMAN Histone deacetylase 2 (sprot)

A histone deacetylase 2 that is encoded in the genome of human.


HDAC7_HUMAN Histone deacetylase 7 (sprot)

A histone deacetylase 7 that is encoded in the genome of human.


RFA1_HUMAN Replication protein A 70 kDa DNA-binding subunit (sprot)

A replication protein A 70 kDa DNA-binding subunit that is encoded in the genome of human.


An amino-acid betaine gamma-aminobutyric acid zwitterion in which all of the hydrogens attached to the nitrogen are replaced by methyl groups.


Major microspecies at pH 7.3.


Carnitine

An amino-acid betaine that is butanoate substituted with a hydroxy group at position C-3 and a trimethylammonium group at C-4.


Conjugate base of porphobilinogen arising from deprotonation of the two carboxy groups and protonation of the amino group; major species at pH 7.3.


The zwitterion formed from 5-aminolevulinic acid by transfer of a proton from the carboxy group to the amino group.  It is the major species present at physiological pH.


PROTOPORPHYRIN

A cyclic tetrapyrrole that consists of porphyrin bearing four methyl substituents at positions 3, 8, 13 and 17, two vinyl substituents at positions 7 and 12 and two 2-carboxyethyl substituents at positions 2 and 18. The parent of the class of protoporphyrins.


succinyl-CoA

An acyl-CoA oxoanion that is the pentaanion of succinyl-CoA, arising from deprotonation of the phosphate, diphosphate and carboxylic acid OH groups.


Ferroprotoporphyrin IX

Heme b in which the iron has oxidation state +2.


Octaanion of preuroporphyrinogen arising from global deprotonation of the eight carboxy groups; major species at pH 7.3.


Farnesyl diphosphate

The trans,trans-stereoisomer of farnesyl diphosphate.


The conjugate base of a 1,2-diacyl-sn-glycero-3-phosphocholine compound formed by deprotonation of the phosphate OH group.


FNTA_HUMAN Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha (sprot)

A protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha that is encoded in the genome of human.


RHOA_HUMAN Transforming protein RhoA (sprot)

A GTP-binding protein RhoA that is encoded in the genome of human.


SC31A_HUMAN Protein transport protein Sec31A (sprot)

A protein transport protein Sec31A that is encoded in the genome of human.


DNLI3_HUMAN DNA ligase 3 (sprot)

A DNA ligase 3 that is encoded in the genome of human.


BAX_HUMAN Apoptosis regulator BAX (sprot)

An apoptosis regulator BAX that is encoded in the genome of human.


RGS2_HUMAN Regulator of G-protein signaling 2 (sprot)

A regulator of G-protein signaling 2 that is encoded in the genome of human.


NADPH

The reduced form of NADP+; used in anabolic reactions, such as lipid and nucleic acid synthesis, which require NADPH as a reducing agent.


An endocannabinoid and an endogenous agonist of the cannabinoid receptors (CB1 and CB2). It is an ester formed from omega-6-arachidonic acid and glycerol.


dCTP tetraanion

A 2'-deoxyribonucleoside 5'-triphosphate(4-) arising from deprotonation of the triphosphate OH groups of 2'-deoxycytidine 5'-triphosphate (dCTP); major species at pH 7.3.


ADP-D-ribose

A nucleotide-sugar having ADP as the nucleotide fragment and D-ribofuranos-5-yl as the sugar component.


A long-chain fatty acid anion resulting from the removal of a proton from the carboxy group of arachidonic acid.


Acetaldehyde

The aldehyde formed from acetic acid by reduction of the carboxy group. It is the most abundant carcinogen in tobacco smoke.


Choline

A choline that is the parent compound of the cholines class, consisting of ethanolamine having three methyl substituents attached to the amino function.


Acetylcholine

Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter.


Ethanolamine

A member of the class of  ethanolamines that is ethane with an amino substituent at C-1 and a hydroxy substituent at C-2, making it both a primary amine and a primary alcohol.


Octaanion of 1D-myo-inositol 1,3,4,5-tetrakisphosphate arising from global deprotonation of the phosphate OH groups; major species at pH 7.3.


nucleoside 5'-triphoshate(4-)

A ribonucleoside triphosphate oxoanion arising from global deprotonation of the  triphosphate groups of any nucleoside triphosphate; major species at pH 7.3.


Deoxyguanosine-triphosphate

A 2'-deoxyribonucleoside 5'-triphosphate(4-) that is the tetraanion of 2'-deoxyguanosine 5'-triphosphate (dGTP), arising from deprotonation of the four triphosphate OH groups; major species at pH 7.3.


Deoxythymidine triphosphate

A 2'-deoxyribonucleoside 5'-triphosphate(4-) obtained by deprotonation of the four triphosphate OH groups of dTTP; major species at pH 7.3.


1,2-diacyl-sn-glycerol 3-phosphate

An sn-glycerol 3-phosphate compound having unspecified O-acyl groups at the 1- and 2-positions.


Chloride ion

A halide anion formed when chlorine picks up an electron to form an an anion.


A 3-sn-glycerophosphoserine compound having acyl substituents at the 1- and 2-hydroxy positions.


Ferriheme

Heme b in which the iron has oxidation state +3.


Oxido nitrite

The nitrogen oxoanion formed by loss of a proton from peroxynitrous acid.


Zwitterionic form of L-citrulline having an anionic carboxy group and a protonated amino group; major species at pH 7.3.


Nitrite

The nitrogen oxoanion formed by loss of a proton from nitrous acid.


A peptide anion obtained by deprotonation of both carboxy groups and protonation of the glutamyl amino group of glutathione; major species at pH 7.3.


Bicarbonate

The carbon oxoanion resulting from the removal of a proton from carbonic acid.


S-Adenosyl-L-methioninamine

Conjugate acid of S-adenosylmethioninamine arising from protonation of the primary amino group.


Zwitterionic form of L-methionine having a anionic carboxy group and a cationic amino group; major species at pH 7.3.


Formate

A monocarboxylic acid anion that is the conjugate base of formic acid. Induces severe metabolic acidosis and ocular injury in human subjects.


2-oxo monocarboxylic acid anion

An oxo monocarboxylic acid anion in which the oxo group is located at the 2-position.


Conjugate base of 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one arising from deprotonation of the 2-hydroxy group.


Spermine (fully protonated form)

An ammonium ion obtained by the protonation of all four amino groups of spermine.


Dianion of S-methyl-5-thio-D-ribulose 1-phosphate.


Dianion of S-methyl-5-thio-alpha-D-ribose 1-phosphate.


An ammonium ion that is the trication of spermidine, formed by protonation at all three nitrogens.


The 2-oxo monocarboxylic acid anion derived from 4-methylthio-2-oxobutanoic acid. The major microspecies at pH 7.3, it is formed from L-methionine via the action of methionine transaminase.


Dianion of 5-(methylsulfanyl)-2,3-dioxopentyl phosphate.


Adenosine with the hydroxy group at C-5' substituted with a methylthio (methylsulfanyl) group.


An alkane-alpha,omega-diammonium(2+) that is the dication of putrescine (1,4-butanediamine) arising from protonation of both primary amino groups; major species at pH 7.3.


threo-Ds-isocitrate

The D-threo-form of isocitrate(3-).


Zwitterionic form of gamma-aminobutyric acid having an anionic carboxy group and a protonated amino group.


The trianion of a 1-phosphatidyl-1D-myo-inositol 5-phosphate.


A phosphatidylinositol 4-phosphate having 1D-myo-configuration.


Zwitterionic form of L-alanine arising from transfer of a proton from the carboxy to the amino group; major species at pH 7.3.


lipid

'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.


long-chain fatty acid

A fatty acid with a chain length ranging from C13 to C22.


electron

Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.


Phenethylamine

A phenylethylamine having the phenyl substituent at the 2-position.


Tetrahydrobiopterin radical cation

An organic radical cation derived from 5,6,7,8-tetrahydrobiopterin.


An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of L-phenylalanine; major species at pH 7.3.


Tetraanion of 7,8-dihydroneopterin 3'-triphosphate.


The conjugate base of monodehydro-L-ascorbic acid arising from deprotonation of the 4-hydroxy group; major species at pH 7.3.


Dyspropterin

A tetrahydropterin  that is 2-amino-5,6,7,8-tetrahydropteridin-4(3H)-one substituted by a 2-oxopropanoyl group at position 6.


A 7,8-dihydrobiopterin in which the 1,2-dihydroxypropyl group has (1S,2R)-configuration.