periplasmic space

definition: The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).


phagolysosome

category: biolink:CellularComponent biolink:AnatomicalEntity biolink:PhysicalEssence biolink:OrganismalEntity biolink:SubjectOfInvestigation biolink:BiologicalEntity biolink:ThingWithTaxon biolink:NamedThing biolink:PhysicalEssenceOrOccurrent

definition: A membrane-bounded intracellular vesicle formed by maturation of an early phagosome following the ingestion of particulate material by phagocytosis; during maturation, phagosomes acquire markers of late endosomes and lysosomes.


early endosome lumen

definition: The volume enclosed by the membrane of an early endosome.


Golgi-associated vesicle lumen

definition: The volume enclosed by the membrane of a Golgi-associated vesicle.


host cell viral assembly compartment

definition: A membrane-bounded compartment that forms in the cytoplasm of the host cell, in which virus assembly takes place.


ciliary base

definition: Area of the cilium (also called flagellum) where the basal body and the axoneme are anchored to the plasma membrane. The ciliary base encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium, and many ciliary proteins localize specifically to this area.


ciliary tip

definition: Part of the cilium where the axoneme ends. The ciliary tip has been implicated in ciliary assembly and disassembly, as well as signal transduction.


ciliary membrane

definition: The portion of the plasma membrane surrounding a cilium.


platelet alpha granule lumen

definition: The volume enclosed by the membrane of the platelet alpha granule.


granular component

definition: A structure found in the nucleolus, which contains nearly completed preribosomal particles destined for the cytoplasm.


lamellar body

definition: A membrane-bounded organelle, specialized for the storage and secretion of various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome.


lamellar body membrane

definition: The lipid bilayer surrounding a lamellar body. A lamellar body is a membrane-bounded organelle, specialized for the storage and secretion of various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome.


photoreceptor outer segment membrane

definition: The membrane surrounding the outer segment of a vertebrate photoreceptor.


photoreceptor disc membrane

definition: Stack of disc membranes located inside a photoreceptor outer segment, and containing densely packed molecules of photoreceptor proteins that traverse the lipid bilayer. Disc membranes arise as evaginations of the ciliary membrane during the development of the outer segment and may or may not remain contiguous with the ciliary membrane.


photoreceptor inner segment membrane

definition: The membrane surrounding the inner segment of a vertebrate photoreceptor. The photoreceptor inner segment contains mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.


sarcoplasmic reticulum membrane

definition: The lipid bilayer surrounding the sarcoplasmic reticulum.


sarcoplasmic reticulum lumen

definition: The volume enclosed by the membranes of the sarcoplasmic reticulum.


sperm flagellum

definition: A microtubule-based flagellum (or cilium) that is part of a sperm, a mature male germ cell that develops from a spermatid.


cornified envelope

definition: A type of plasma membrane that has been modified through addition of distinct intracellular and extracellular components, including ceramide, found in cornifying epithelial cells (corneocytes).


macropinosome membrane

definition: The lipid bilayer surrounding a macropinosome.


cytolytic granule lumen

definition: Any cytoplasmic membrane-bounded vesicle lumen that is part of a cytolytic granule.


multivesicular body lumen

definition: The volume enclosed by the outermost membrane of a multivesicular body.


basolateral plasma membrane

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


apical plasma membrane

definition: The region of the plasma membrane located at the apical end of the cell.


platelet dense granule lumen

definition: The volume enclosed by the membrane of the platelet dense granule.


platelet dense granule membrane

definition: The lipid bilayer surrounding the platelet dense granule.


viral tegument

definition: A structure lying between the capsid and envelope of a virus, varying in thickness and often distributed asymmetrically.


Golgi-associated vesicle

definition: Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.


ciliary basal body

definition: A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodeling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport.


recycling endosome

definition: An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.


microvillus membrane

definition: The portion of the plasma membrane surrounding a microvillus.


microvillus

definition: Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.


autophagosome

definition: A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the lytic vacuole/lysosome for degradation as part of macroautophagy.


multivesicular body, internal vesicle

definition: A membrane-bounded vesicle wholly contained within a multivesicular body.


regulation of cell cycle

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

definition: Any process that modulates the rate or extent of progression through the cell cycle.


DNA replication

definition: The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.


telomere maintenance via telomerase

definition: The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase.


name: telomere maintenance via semi-conservative replication

definition: 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.


name: regulation of mitotic cell cycle phase transition

definition: Any process that modulates the frequency, rate or extent of mitotic cell cycle phase transition.


name: proteasome-mediated ubiquitin-dependent protein catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.


name: positive regulation of epidermal growth factor receptor signaling pathway

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


name: positive regulation of transcription by RNA polymerase II

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


Notch signaling pathway

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

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


name: positive regulation of transcription of Notch receptor target

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


name: positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction

definition: Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase/protein kinase B signal transduction.


angiotensin maturation

definition: The process leading to the attainment of the full functional capacity of angiotensin by conversion of angiotensinogen into mature angiotensin in the blood.


name: positive regulation of neurotrophin TRK receptor signaling pathway

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


name: phosphatidylinositol 3-kinase/protein kinase B signal transduction

definition: An intracellular signaling cassette that starts with phosphatidylinositol 3-kinase (PI3K) activation, production of phosphatidylinositol 3-phosphate (PI3P), activation of PDK1, which recruits and ending with the activation of protein kinase B (PKB, also known as Akt). PI3K is activated by cell surface receptors. Note that PTEN is an inhibitor of the pathway.


name: mitotic spindle assembly checkpoint signaling

definition: A mitotic cell cycle checkpoint that delays mitotic sister chromatid separation and consequently the mitotic metaphase/anaphase transition until the spindle is correctly assembled and chromosomes are attached to the spindle. Spindle assembly checkpoint signaling begins with the activated Mph family kinase, and results in the inhibition of the Anaphase Promoting Complex and its activator Sleepy/Cdc20 by the mitotic checkpoint complex (MCC).


sister chromatid cohesion

definition: The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.


pre-replicative complex assembly

definition: The aggregation, arrangement and bonding together of a set of components to form the pre-replicative complex, a protein-DNA complex that forms at the origin of replication during the initial step of DNA replication and allows the origin to become competent, or 'licensed', for replication.


mitotic G1 phase

definition: The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis.


name: negative regulation of transcription by RNA polymerase II

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


name: negative regulation of transforming growth factor beta receptor signaling pathway

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


name: transforming growth factor beta receptor signaling pathway

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


name: regulation of type II interferon-mediated signaling pathway

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


name: type II interferon-mediated signaling pathway

definition: 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.


DNA-templated transcription

definition: The synthesis of an RNA transcript from a DNA template.


spliceosomal snRNP assembly

definition: 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.


complement activation

definition: Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.


complement activation, lectin pathway

definition: 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.


name: complement activation, classical pathway

definition: Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.


name: complement activation, alternative pathway

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


regulation of complement activation

definition: Any process that modulates the frequency, rate or extent of complement activation.


name: nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway

definition: The series of molecular signals initiated by a ligand binding to a nucleotide-binding domain, leucine rich repeat containing receptor (NLR), and ending with the regulation of a downstream cellular process. NLRs are cytoplasmic receptors defined by their tripartite domain architecture that contains: a variable C-terminus, a middle nucleotide-binding domain, and a LRR domain that is variable in the repeats composition and number.


name: negative regulation of type I interferon production

definition: Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.


name: positive regulation of canonical NF-kappaB signal transduction

definition: Any process that activates or increases the frequency, rate or extent of a canonical NF-kappaB signaling cascade.


apoptotic signaling pathway

definition: The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.


JNK cascade

definition: A MAPK cascade containing at least the JNK (MAPK8) MAP kinase. It starts with the activation of JUN3K (a MAPK3K), which activates JNKK a MAP2K), which in turn activates JNK. The cascade can also contain an additional tier: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinases in the downstream tier. The JNK cascade is activated by stress signals, as well as by G protein-coupled receptors, growth factors, and cytokines, and results in cellular responses such as cell proliferation, cell differentiation, apoptosis and inflammation.


p38MAPK cascade

definition: A MAPK cascade containing at least the p38MAPK (MAPK14) MAP kinase, or Hog1 in yeast. It starts with the activation of a MAP3K, and the consecutive activation of a MPK2K and of p38MAPK. The cascade can also contain an additional tier: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinases in the downstream tier. The p38MAPK cascade is activated by stress signals, including hyperosmolarity, as well as by G protein-coupled receptors, growth factors, and cytokines, and results in cellular responses such as cell proliferation, cell differentiation, apoptosis and inflammation.


ERK1 and ERK2 cascade

definition: A MAPK cascade containing at least the ERK1 or ERK2 MAP kinases. It starts with the activation of a MAP3K, and the consecutive activation of a MPK2K and of ERK1 or ERK2. The cascade can also contain an additional tier: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinase in the downstream tier. The ERK1/ERK2 cascade is activated by mitogens, growth factors, G protein-coupled receptors, and results in cellular responses such as cell proliferation, cell differentiation and development.


stress-activated MAPK cascade

definition: A MAPK cascade that starts with the activation of a stress-activated MAP kinase cascade.


name: activation of NF-kappaB-inducing kinase activity

definition: The stimulation of the activity of NF-kappaB-inducing kinase through phosphorylation at specific residues.


name: MyD88-dependent toll-like receptor signaling pathway

definition: A toll-like receptor signaling pathway in which the MyD88 adaptor molecule mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate an innate immune response.


toll-like receptor 5 signaling pathway

definition: The series of molecular signals initiated by a ligand binding to toll-like receptor 5.


necroptotic process

definition: A programmed necrotic cell death process which begins when a cell receives a signal (e.g. a ligand binding to a death receptor or to a Toll-like receptor), and proceeds through a series of biochemical events (signaling pathways), characterized by activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3, also called RIP1/3) and by critical dependence on mixed lineage kinase domain-like (MLKL), and which typically lead to common morphological features of necrotic cell death. The process ends when the cell has died. The process is divided into a signaling phase, and an execution phase, which is triggered by the former.


name: TRIF-dependent toll-like receptor signaling pathway

definition: The series of molecular signals initiated by a ligand binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate an innate immune response.


canonical NF-kappaB signal transduction

definition: An intracellular signaling cassette characterized by the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB, also known as the canonical NF-kappaB signaling cascade. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription. The canonical NF-kappaB pathway is mainly stimulated by proinflammatory cytokines such as IL-1beta, tumor necrosis factor (TNF)-alpha, antigen ligands, and toll-like receptors (TLRs).


regulation of necroptotic process

definition: Any process that modulates the rate, frequency or extent of a necroptotic process, a necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.


name: negative regulation of cysteine-type endopeptidase activity involved in apoptotic process

definition: Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.


apoptotic DNA fragmentation

definition: 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.


execution phase of apoptosis

definition: A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.


name: negative regulation of apoptotic process

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


regulation of apoptotic process

definition: Any process that modulates the occurrence or rate of cell death by apoptotic process.


name: positive regulation of establishment of protein localization to mitochondrion

definition: Any process that activates or increases the frequency, rate or extent of establishment of protein localization to mitochondrion.


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

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


name: positive regulation of intrinsic apoptotic signaling pathway

definition: Any process that activates or increases the frequency, rate or extent of intrinsic apoptotic signaling pathway.


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

definition: 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.


name: regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction

definition: Any process that modulates the frequency, rate or extent of phosphatidylinositol 3-kinase/protein kinase B signal transduction.


T cell costimulation

definition: 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.


Ras protein signal transduction

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


definition: The series of molecular signals initiated by interleukin-15 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


definition: The series of molecular signals initiated by interleukin-9 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


definition: The series of molecular signals initiated by interleukin-2 binding to its receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


definition: The series of molecular signals initiated by interleukin-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.


cytokine-mediated signaling pathway

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


chemical synaptic transmission

definition: The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.


regulation of NMDA receptor activity

definition: Any process that modulates the frequency, rate or extent of N-methyl-D-aspartate selective glutamate receptor activity.


activation of protein kinase A activity

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


nitric oxide metabolic process

definition: The chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.


tetrahydrobiopterin metabolic process

definition: The chemical reactions and pathways involving tetrahydrobiopterin, the reduced form of biopterin (2-amino-4-hydroxy-6-(1,2-dihydroxypropyl)-pteridine). It functions as a hydroxylation coenzyme, e.g. in the conversion of phenylalanine to tyrosine.


ubiquinone biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.


transferrin transport

definition: 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.


intracellular iron ion homeostasis

definition: A homeostatic process involved in the maintenance of a steady state level of iron ions within a cell.


metabolic process

definition: The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.


T cell receptor signaling pathway

definition: The series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.


name: fibroblast growth factor receptor signaling pathway

definition: The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.


MAPK cascade

definition: An intracellular protein kinase cascade containing at least a MAP kinase (MAPK). It starts with the activation of a MAP3K, and the consecutive activation of a MPK2K and a MAPK. The cascade can also contain an additional tier: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinase in the downstream tier to transmit a signal within a cell.


name: small GTPase-mediated signal transduction

definition: An intracellular signaling cassette in which a small monomeric GTPase relays a signal.


name: positive regulation of apoptotic process

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


name: regulation of cysteine-type endopeptidase activity involved in apoptotic process

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


positive regulation of axonogenesis

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


negative regulation of axonogenesis

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


regulation of axonogenesis

definition: Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron.


name: membrane protein intracellular domain proteolysis

definition: The proteolytic cleavage of a transmembrane protein leading to the release of an intracellular domain.


name: neurotrophin TRK receptor signaling pathway

definition: 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.


negative regulation of cell cycle

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


microtubule-based movement

definition: A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.


name: activation of adenylate cyclase activity

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


name: cell surface receptor protein tyrosine kinase signaling pathway

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


nerve growth factor processing

definition: The generation of a mature nerve growth factor (NGF) by proteolysis of a precursor.


G1/S transition of mitotic cell cycle

definition: The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.


positive regulation of DNA replication

definition: Any process that activates or increases the frequency, rate or extent of DNA replication.


name: positive regulation of receptor signaling pathway via JAK-STAT

definition: Any process that activates or increases the frequency, rate or extent of the JAK-STAT signaling pathway activity.


name: negative regulation of signal transduction

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


positive regulation of cell cycle

definition: Any process that activates or increases the rate or extent of progression through the cell cycle.


extracellular matrix disassembly

definition: A process that results in the breakdown of the extracellular matrix.


name: regulation of androgen receptor signaling pathway

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


name: Fc-gamma receptor signaling pathway involved in phagocytosis

definition: An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.


name: negative regulation of mitotic cell cycle

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


name: regulation of cell cycle G2/M phase transition

definition: 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.


name: regulation of G2/M transition of mitotic cell cycle

definition: 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 mitotic cell cycle.


regulation of mitotic cell cycle

definition: Any process that modulates the rate or extent of progress through the mitotic cell cycle.


G2/M transition of mitotic cell cycle

definition: The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.


name: DNA strand elongation involved in DNA replication

definition: The process in which an existing DNA strand is extended by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication.


name: metaphase/anaphase transition of mitotic cell cycle

definition: The cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin.


mitotic nuclear membrane reassembly

definition: The mitotic cell cycle process involving ESCRTIII that results in reformation of the nuclear envelope after mitotic nuclear division. In organisms undergoing closed mitosis this involves resealing or 'repair' of the nuclear envelope in the nuclear bridge.


mitotic sister chromatid separation

definition: The process in which sister chromatids are physically detached from each other during mitosis.


name: regulation of mitotic spindle organization

definition: Any process that modulates the rate, frequency or extent of the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.


mitotic chromosome condensation

definition: The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells.


mitotic spindle organization

definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.


mitotic sister chromatid segregation

definition: The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.


mitotic nuclear membrane disassembly

definition: The mitotic cell cycle process in which the controlled partial or complete breakdown of the nuclear membranes during occurs during mitosis.


Golgi inheritance

definition: The partitioning of Golgi apparatus between daughter cells at cell division.


intrinsic apoptotic signaling pathway

definition: The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP).


cellular response to cytokine stimulus

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


definition: The series of molecular signals initiated by interleukin-33 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


definition: The series of molecular signals initiated by interleukin-1 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


definition: The series of molecular signals initiated by interleukin-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.


name: adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway

definition: 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).


name: negative regulation of epidermal growth factor receptor signaling pathway

definition: Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.


signal transduction

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


name: epidermal growth factor receptor signaling pathway

definition: The series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.


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

definition: 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.


name: double-strand break repair via synthesis-dependent strand annealing

definition: SDSA is a major mechanism of double-strand break repair in mitosis which allows for the error-free repair of a double-strand break without the exchange of adjacent sequences. The broken DNA searches for and base pairs with a homologous region in an intact chromosome. DNA synthesis initiates from the 3' end of the invading DNA strand, using the intact chromosome as the template. Newly synthesized DNA is then displaced from the template and anneal with its complement on the other side of the double-strand break.


name: double-strand break repair via nonhomologous end joining

definition: The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.


cell cycle checkpoint signaling

definition: A signaling process that controls cell cycle progression by monitoring the integrity of specific cell cycle events. A cell cycle checkpoint begins with detection of deficiencies or defects and ends with signal transduction.


name: beta-catenin destruction complex disassembly

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


beta-catenin-TCF complex assembly

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


name: negative regulation of canonical Wnt signaling pathway

definition: Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.


name: Wnt signaling pathway, planar cell polarity pathway

definition: A type of non-canonical Wnt signaling pathway in which Wnt binding to its receptor on the surface of a target cell results in the activation small G proteins such as Rho, Rac, and Cdc42 which, in turn activate effectors, including C-Jun N-terminal kinase (JNK) and Rho kinase (Rok). The signaling ends with change in the transcription of target genes and/or reorganisation of the cytoskeleton.


name: Wnt signaling pathway, calcium modulating pathway

definition: A type of non-canonical Wnt signaling in which Wnt binding to its receptor on the surface of a target cell leads to an increase in intracellular calcium and activation of protein kinase C (PKC).


non-canonical Wnt signaling pathway

definition: A type of Wnt signaling pathway in which Wnt binding to its receptor on the surface of a target cell results in the by propagation of the molecular signals via effectors other than beta-catenin.


metanephric nephron development

definition: The process whose specific outcome is the progression of a nephron in the metanephros over time, from its formation to the mature structure. A nephron is the functional unit of the kidney.


name: positive regulation of canonical Wnt signaling pathway

definition: Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.


ureteric bud formation

definition: The developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct. This process begins when the bud protrudes from the duct and ends when it is a recognizable bud.


name: regulation of signal transduction by p53 class mediator

definition: Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.


definition: The series of molecular signals initiated by interleukin-6 binding to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


name: regulation of extrinsic apoptotic signaling pathway via death domain receptors

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


name: activation of cysteine-type endopeptidase activity involved in apoptotic process

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


name: symbiont-mediated suppression of host apoptosis

definition: A process in which a symbiont inhibits or disrupts the normal execution of host apoptosis, leading to a decrease in the frequency, rate or extent of apoptosis in the host cell. The host is defined as the larger of the organisms involved in a symbiotic interaction.


name: regulation of tumor necrosis factor-mediated signaling pathway

definition: Any process that modulates the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.


name: positive regulation of ceramide biosynthetic process

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


name: death-inducing signaling complex assembly

definition: 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.


name: tumor necrosis factor-mediated signaling pathway

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


name: MyD88-independent toll-like receptor signaling pathway

definition: A toll-like receptor signaling pathway not relying on the MyD88 adaptor molecule. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate an immune response.


name: extrinsic apoptotic signaling pathway in absence of ligand

definition: The series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.


extrinsic apoptotic signaling pathway

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


apoptotic process

definition: A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.


programmed necrotic cell death

definition: A necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.


cell surface receptor signaling pathway

definition: The series of molecular signals initiated by an extracellular ligand binding to a receptor located on the cell surface. The pathway ends with regulation of a downstream cellular process, e.g. transcription.


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

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


leukocyte migration

definition: The movement of a leukocyte within or between different tissues and organs of the body.


insulin receptor signaling pathway

definition: The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.


ERBB2 signaling pathway

definition: 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.


regulation of cell motility

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


name: regulation of DNA-templated transcription

definition: Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.


name: miRNA-mediated post-transcriptional gene silencing

definition: A post-transcriptional gene silencing pathway in which regulatory microRNAs (miRNAs) elicit silencing of specific target genes. miRNAs are endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate protein production by either of two posttranscriptional mechanisms: endonucleolytic cleavage of the RNA (often mRNA) or mRNA translational repression, usually accompanied by poly-A tail shortening and subsequent degradation of the mRNA. miRNAs are present in all the animals and in plants, whereas siRNAs are present in lower animals and in plants.


name: regulation of cell-cell adhesion mediated by cadherin

definition: Any process that modulates the frequency, rate or extent of cell-cell adhesion mediated by cadherin.


adherens junction organization

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


bicellular tight junction assembly

definition: 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.


hemidesmosome assembly

definition: 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.


cell junction assembly

definition: A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction.


definition: 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.


name: nucleotide-excision repair, DNA damage recognition

definition: 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.


name: nucleotide-excision repair, DNA gap filling

definition: 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.


name: global genome nucleotide-excision repair

definition: The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.


name: double-strand break repair via homologous recombination

definition: The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.


interstrand cross-link repair

definition: Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA. DNA interstrand crosslinks occur when both strands of duplex DNA are covalently tethered together (e.g. by an exogenous or endogenous agent), thus preventing the strand unwinding necessary for essential DNA functions such as transcription and replication.


toll-like receptor 10 signaling pathway

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


toll-like receptor 3 signaling pathway

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


neurotransmitter transport

definition: 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.


name: gamma-aminobutyric acid catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms.


name: gamma-aminobutyric acid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms.


gamma-aminobutyric acid reuptake

definition: The uptake of gamma-aminobutyric acid (GABA, 4-aminobutyrate) by neurons or glial cells. This process leads to inactivation and recycling of neurotransmitters.


neurotransmitter uptake

definition: The directed movement of neurotransmitters into neurons or glial cells. This process leads to inactivation and recycling of neurotransmitters.


membrane depolarization

definition: The process in which membrane potential decreases with respect to its steady-state potential, usually from negative potential to a more positive potential. For example, the initial depolarization during the rising phase of an action potential is in the direction from the negative steady-state resting potential towards the positive membrane potential that will be the peak of the action potential.


neurotransmitter secretion

definition: The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission.


cellular response to oxidative stress

definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.


name: purine ribonucleoside monophosphate biosynthetic process

definition: 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.


name: pyrimidine nucleoside biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).


diphosphate metabolic process

definition: The chemical reactions and pathways involving diphosphate, the anion or salt of diphosphoric acid.


name: nucleobase-containing small molecule biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.


name: nucleobase-containing small molecule catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.


name: nucleobase-containing small molecule metabolic process

definition: The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.


purine nucleotide catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.


pyrimidine nucleoside catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).


name: nucleobase-containing small molecule interconversion

definition: The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.


purine-containing compound salvage

definition: Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.


pyrimidine nucleoside salvage

definition: Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.


glycogen biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.


glycogen catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.


glycogen metabolic process

definition: The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.


name: 5-phosphoribose 1-diphosphate biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.


pentose-phosphate shunt

definition: The metabolic process in which glucose-6-phosphate is oxidized to form carbon dioxide (CO2) and ribulose 5-phosphate, coupled to reduction of NADP+ to NADPH; ribulose 5-P then enters a series of reactions that can yield biosynthetic precursors (ribose-5-phosphate and erythrose-4-phosphate) and glycolytic intermediates (fructose-6-phosphate and glyceraldehyde-3-phosphate).


name: galactose catabolic process via UDP-galactose

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


fructose biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of fructose, the ketohexose arabino-2-hexulose.


name: fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate

definition: The chemical reactions and pathways resulting in the breakdown of fructose that results in the formation of dihydroxyacetone phosphate and glyceraldehyde-3-phosphate.


fructose metabolic process

definition: The chemical reactions and pathways involving fructose, the ketohexose arabino-2-hexulose. Fructose exists in a open chain form or as a ring compound. D-fructose is the sweetest of the sugars and is found free in a large number of fruits and honey.


name: cholesterol biosynthetic process via desmosterol

definition: The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, via the intermediate desmosterol.


name: cholesterol biosynthetic process via lathosterol

definition: The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, via the intermediate lathosterol.


cholesterol biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.


vitamin D metabolic process

definition: 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).


endoplasmic reticulum mannose trimming

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


protein folding

definition: The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.


COPII vesicle coating

definition: The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.


name: endoplasmic reticulum to Golgi vesicle-mediated transport

definition: The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.


Golgi apparatus mannose trimming

definition: Any protein alpha-1,2-demannosylation that takes place in the Golgi apparatus.


GDP-mannose biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine diphosphate.


definition: The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.


name: dolichyl diphosphate biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of dolichyl diphosphate, a diphosphorylated dolichol derivative.


name: protein N-linked glycosylation via asparagine

definition: 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.


GDP-L-fucose biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of GDP-L-fucose, a substance composed of L-fucose in glycosidic linkage with guanosine diphosphate.


sphingolipid catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).


sphingolipid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).


glycosphingolipid catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide.


glycosphingolipid biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide.


glycosphingolipid metabolic process

definition: The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide.


name: adenylate cyclase-activating G protein-coupled receptor signaling pathway

definition: A G protein-coupled receptor signaling pathway in which the signal is transmitted via the activation of adenylyl cyclase activity which results in an increase in the intracellular concentration of cyclic AMP (cAMP). This pathway is negatively regulated by phosphodiesterase, which cleaves cAMP and terminates the signaling.


arachidonic acid metabolic process

definition: The chemical reactions and pathways involving arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer.


name: G protein-coupled receptor signaling pathway

definition: The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane.


ceramide transport

definition: The directed movement of ceramides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ceramides are a class of lipid composed of sphingosine linked to a fatty acid.


sphingolipid metabolic process

definition: The chemical reactions and pathways involving sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).


name: dolichol-linked oligosaccharide biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of dolichol-linked oligosaccharide, usually by a stepwise addition of glycosyl chains to endoplasmic reticulum membrane-bound dolichol-P.


glycosaminoglycan metabolic process

definition: The chemical reactions and pathways involving glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.


keratan sulfate catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of keratan sulfate, a glycosaminoglycan with repeat units consisting of beta-1,4-linked D-galactopyranosyl-beta-(1,4)-N-acetyl-D-glucosamine 6-sulfate and with variable amounts of fucose, sialic acid and mannose units; keratan sulfate chains are covalently linked by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylose to peptidyl-threonine or serine residues.


keratan sulfate biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of keratan sulfate, a glycosaminoglycan with repeat units consisting of beta-1,4-linked D-galactopyranosyl-beta-(1,4)-N-acetyl-D-glucosamine 6-sulfate and with variable amounts of fucose, sialic acid and mannose units; keratan sulfate chains are covalently linked by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylose to peptidyl-threonine or serine residues.


keratan sulfate metabolic process

definition: The chemical reactions and pathways involving keratan sulfate, a glycosaminoglycan with repeat units consisting of beta-1,4-linked D-galactopyranosyl-beta-(1,4)-N-acetyl-D-glucosamine 6-sulfate and with variable amounts of fucose, sialic acid and mannose units; keratan sulfate chains are covalently linked by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylose to peptidyl-threonine or serine residues.


name: heparan sulfate proteoglycan biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues; the former are a mixture of sulfated and nonsulfated D-glucuronic acid and L-iduronic acid; the L-iduronic acid is either sulfated or acetylated on its amino group as well as being sulfated on one of its hydroxyl groups; heparan sulfate chains are covalently linked to peptidyl-serine by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylosyl to serine residues.


name: heparan sulfate proteoglycan catabolic process

definition: 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.


dermatan sulfate biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of dermatan sulfate, any glycosaminoglycan with repeats consisting of beta-(1,4)-linked L-iduronyl-beta-(1,3)-N-acetyl-D-galactosamine 4-sulfate units.


name: chondroitin sulfate biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate.


glycosaminoglycan catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars.


chondroitin sulfate metabolic process

definition: The chemical reactions and pathways involving chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate. They usually occur linked to a protein to form proteoglycans. Two subgroups exist, one in which the sulfate is on the 4-position (chondroitin sulfate A) and the second in which it is in the 6-position (chondroitin sulfate C). They often are polydisperse and often differ in the degree of sulfation from tissue to tissue. The chains of repeating disaccharide are covalently linked to the side chains of serine residues in the polypeptide backbone of a protein by a glycosidic attachment through the trisaccharide unit galactosyl-galactosyl-xylosyl. Chondroitin sulfate B is more usually known as dermatan sulfate.


hyaluronan biosynthetic process

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


hyaluronan catabolic process

definition: 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.


hyaluronan metabolic process

definition: The chemical reactions and pathways involving 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.


oligosaccharide catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.


name: glucuronate catabolic process to xylulose 5-phosphate

definition: The chemical reactions and pathways resulting in the breakdown of glucuronate into other compounds, including xylulose 5-phosphate.


regulation of glycolytic process

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


name: regulation of glycolytic process through fructose-6-phosphate

definition: Any process that modulates the frequency, rate or extent of glycolytic process through fructose-6-phosphate.


canonical glycolysis

definition: The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP.


name: acetyl-CoA biosynthetic process from pyruvate

definition: The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate.


name: regulation of small molecule metabolic process

definition: Any process that modulates the rate, frequency or extent of a small molecule metabolic process.


name: regulation of acetyl-CoA biosynthetic process from pyruvate

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


ferredoxin metabolic process

definition: 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.


iron-sulfur cluster assembly

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


succinyl-CoA biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of succinyl-CoA.


fatty acid alpha-oxidation

definition: A metabolic pathway by which 3-methyl branched fatty acids are degraded. These compounds are not degraded by the normal peroxisomal beta-oxidation pathway, because the 3-methyl blocks the dehydrogenation of the hydroxyl group by hydroxyacyl-CoA dehydrogenase. The 3-methyl branched fatty acid is converted in several steps to pristenic acid, which can then feed into the beta-oxidative pathway.


name: fatty acid beta-oxidation using acyl-CoA oxidase

definition: A fatty acid beta-oxidation pathway in which the initial step, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA oxidase; the electrons removed by oxidation pass directly to oxygen and produce hydrogen peroxide, which is cleaved by peroxisomal catalases. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).


fatty acid catabolic process

definition: 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.


bicarbonate transport

definition: 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.


amino acid transport

definition: The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.


name: long-chain fatty-acyl-CoA biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of a long-chain fatty-acyl-CoA any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons.


fatty-acyl-CoA biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of a fatty-acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty-acyl group.


name: branched-chain amino acid catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.


lysine catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of lysine, 2,6-diaminohexanoic acid.


glycine catabolic process

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


carboxylic acid metabolic process

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


fatty acid beta-oxidation

definition: A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).


name: short-chain fatty acid catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of a short-chain fatty acid. A short-chain fatty acid has an aliphatic tail containing fewer than 6 carbons.


L-phenylalanine metabolic process

definition: The chemical reactions and pathways involving L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.


tyrosine catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.


aromatic amino acid metabolic process

definition: The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).


2-oxoglutarate metabolic process

definition: The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.


L-serine biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.


monoatomic ion transport

definition: The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.


name: mitochondrial respiratory chain complex III assembly

definition: The aggregation, arrangement and bonding together of a set of components to form the cytochrome bc(1) complex (also known as ubiquinol-cytochrome c reductase), in the mitochondrial inner membrane.


mitochondrial translational elongation

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


mitochondrial translational termination

definition: 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).


mitochondrial translational initiation

definition: 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.


heme catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.


heme biosynthetic process

definition: 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.


receptor-mediated endocytosis

definition: 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.


heme metabolic process

definition: The chemical reactions and pathways involving heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.


name: porphyrin-containing compound metabolic process

definition: The chemical reactions and pathways involving any member of a large group of derivatives or analogs of porphyrin. Porphyrins consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.


name: mitochondrial cytochrome c oxidase assembly

definition: The aggregation, arrangement and bonding together of a set of components to form respiratory chain complex IV (also known as cytochrome c oxidase) in the mitochondrial inner membrane.


proline catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.


name: aspartate family amino acid metabolic process

definition: The chemical reactions and pathways involving amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine.


agmatine biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of agmatine ((4-aminobutyl)guanidine, NH2-CH2-CH2-CH2-CH2-NH-C(-NH2)(=NH)). Agmatine is the decarboxylation product of the amino acid arginine and is an intermediate in polyamine biosynthesis. It is synthesized in the brain, stored in synaptic vesicles, accumulated by uptake, released by membrane depolarization, and inactivated by agmatinase.


polyamine biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.


name: regulation of cellular amino acid metabolic process

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


polyamine metabolic process

definition: The chemical reactions and pathways involving polyamines, any organic compound containing two or more amino groups.


L-histidine catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.

description: The chemical reactions and pathways resulting in the breakdown of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.


name: NAD biosynthesis via nicotinamide riboside salvage pathway

definition: The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD) from the vitamin precursor nicotinamide riboside.


NAD metabolic process

definition: The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.


tryptophan catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.


selenium compound metabolic process

definition: The chemical reactions and pathways involving compounds that contain selenium, such as selenocysteine.


selenocysteine metabolic process

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


name: L-threonine catabolic process to glycine

definition: The chemical reactions and pathways resulting in the breakdown of L-threonine (the L-enantiomer of 2-amino-3-hydroxybutyric acid) to form to form 2-amino-3-oxobutanoate, which is subsequently converted to glycine.


name: glutamine family amino acid metabolic process

definition: The chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline.


protein targeting to mitochondrion

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


lactose biosynthetic process

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


oligosaccharide biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.


peptide biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.


carbohydrate metabolic process

definition: The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.


pyruvate metabolic process

definition: The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.


glucose metabolic process

definition: The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.


tricarboxylic acid cycle

definition: A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.


melanin biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom.


name: pyruvate family amino acid metabolic process

definition: The chemical reactions and pathways involving any amino acid that requires pyruvate for its synthesis, e.g. alanine.


creatine metabolic process

definition: The chemical reactions and pathways involving creatine (N-(aminoiminomethyl)-N-methylglycine), a compound synthesized from the amino acids arginine, glycine, and methionine that occurs in muscle.


carnitine biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.


choline catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine.


catecholamine biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.


indolalkylamine biosynthetic process

definition: The chemical reactions and pathways resulting in the formation of indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group.


thyroid hormone metabolic process

definition: The chemical reactions and pathways involving any of the compounds secreted by the thyroid gland, largely thyroxine and triiodothyronine.


thyroid hormone generation

definition: The formation of either of the compounds secreted by the thyroid gland, mainly thyroxine and triiodothyronine. This is achieved by the iodination and joining of tyrosine molecules to form the precursor thyroglobin, proteolysis of this precursor gives rise to the thyroid hormones.


name: organonitrogen compound metabolic process

definition: The chemical reactions and pathways involving organonitrogen compound.


name: L-methionine salvage from methylthioadenosine

definition: The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.


name: sulfide oxidation, using sulfide:quinone oxidoreductase

definition: A sulfide oxidation process that proceeds via the reaction catalyzed by sulfide:quinone oxidoreductase.


sulfur amino acid catabolic process

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


transsulfuration

definition: The interconversion of homocysteine and cysteine via cystathionine. In contrast with enteric bacteria and mammals, Saccharomyces cerevisiae has two transsulfuration pathways employing two separate sets of enzymes.


sulfur amino acid metabolic process

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


name: mitochondrial respiratory chain complex I assembly

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


adaptive thermogenesis

definition: The regulated production of heat in response to short term environmental changes, such as stress, diet or reduced temperature.


proton transmembrane transport

definition: The directed movement of a proton across a membrane.


name: proton motive force-driven mitochondrial ATP synthesis

definition: The transport of protons across a mitochondrial membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.


cellular metabolic process

definition: The chemical reactions and pathways by which individual cells transform chemical substances.


respiratory electron transport chain

definition: A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.


Fc-epsilon receptor signaling pathway

definition: 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.


name: insulin-like growth factor receptor signaling pathway

definition: The series of molecular signals initiated by a ligand binding to an insulin-like growth factor receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


name: positive regulation of extrinsic apoptotic signaling pathway in absence of ligand

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


name: positive regulation of Ras protein signal transduction

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


name: positive regulation of tau-protein kinase activity

definition: Any process that activates or increases the frequency, rate or extent of tau-protein kinase activity.


mRNA export from nucleus

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


name: nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay

definition: A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.


name: nuclear-transcribed mRNA poly(A) tail shortening

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


name: stimulatory C-type lectin receptor signaling pathway

definition: The series of molecular signals initiated by the binding of C-type lectin to its receptor on the surface of a target cell, and resulting in cellular activation.


name: cytoplasmic pattern recognition receptor signaling pathway

definition: The series of molecular signals initiated by the binding of a ligand from another organism to a cytoplasmic pattern recognition receptor (PRR). PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species.


name: toll-like receptor TLR1:TLR2 signaling pathway

definition: 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.


name: toll-like receptor TLR6:TLR2 signaling pathway

definition: The series of molecular signals initiated by a ligand binding of a heterodimeric TLR6: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.


toll-like receptor 2 signaling pathway

definition: The series of molecular signals initiated by a ligand binding to toll-like receptor 2.


name: regulation of toll-like receptor signaling pathway

definition: Any process that modulates the frequency, rate, or extent of toll-like receptor signaling pathway.


toll-like receptor 9 signaling pathway

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


toll-like receptor signaling pathway

definition: 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.


toll-like receptor 4 signaling pathway

definition: The series of molecular signals initiated by a ligand binding to toll-like receptor 4.


name: positive regulation of type I interferon production

definition: Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.


name: regulation of type I interferon production

definition: Any process that modulates the frequency, rate, or extent of interferon type I production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.


antimicrobial humoral response

definition: An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus.


name: symbiont defense to host-produced reactive oxygen species

definition: A process in which a symbiont alters or subverts either the host signal transduction pathways leading to the production of reactive oxygen species as part of the host innate immune response.


name: siderophore-dependent iron import into cell

definition: A process in which iron (Fe3+) is solubilized by ferric iron-specific chelators, known as siderophores, excreted by a cell; the iron-siderophore complex is then transported into the cell by specific cell surface receptors.


name: symbiont-mediated detoxification of host-generated reactive oxygen species

definition: A process in which a symbiont interferes with, inhibits or disrupts the host reactive oxygen species (ROS)-mediated innate immune response by directly degrading host ROS. The host is defined as the larger of the organisms involved in a symbiotic interaction.


response to host immune response

definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detecting the immune response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.


name: vascular endothelial growth factor receptor signaling pathway

definition: The series of molecular signals initiated by a ligand binding to a vascular endothelial growth factor receptor (VEGFR) on the surface of the target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.


name: virus-mediated perturbation of host defense response

definition: A process in which a virus interferes with the ability of the host to mount a defense in response to its presence. Host defenses may be induced by the presence of the virus or may be preformed (e.g. physical barriers). The host is defined as the larger of the organisms involved in a symbiotic interaction.


symbiont entry into host cell

definition: The process by which a symbiont breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the symbiont or its genome is released into the host cell.