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Comment: Migrated to Confluence 5.3

Activity functions are applied to protein, complex, and RNA abundances to specify the frequency of events resulting from the molecular activity of the abundance. Activity functions provide distinct terms that differentiate the molecular activity from the abundance of a protein, complex, or RNA.

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catalyticActivity(), cat()

For the abundance term A, catalyticActivity(A) or cat(A) denotes the frequency or abundance of events in which a member of A acts as an enzymatic catalyst of biochemical reactions; A should represent an abundance of a protein, molecular complex, or ribozyme with catalytic activity, such as super oxide dismutase 1 (p(HGNC:SOD1)) or the RNA polymerase II complex (complex(NCH:"RNA polymerase II complex") ).
In BEL V1.0, certain types of catalytic activity are represented by a more specific activity function. These include kinase (phosphotransferase), ADP-ribosylase, phosphatase, and peptidase (protease). To represent these types of activities, the more specific function should be used.

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chaperoneActivity(), chap()

For the abundance term A, chaperoneActivity(A) or chap(A) denotes the frequency or abundance of events in which a member of A acts as a chaperone facilitating the folding, unfolding, assembly, or disassembly of another protein. A should represent an abundance of a protein or molecular complex with chaperone activity, such as Hsp27 (p(HGNC:HSPB1)) or BiP (p(HGNC:HSPA5)).

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gtpBoundActivity(), gtp()

For the protein abundance term A, gtpBoundActivity(A) or gtp(A) denotes the frequency or abundance of events that a member of the protein abundance A acts in due to its being in the active, GTP-bound state. A should represent the protein abundance of a GTP-binding protein, such as G-ALPHA-q (p(HGNC:GNAQ)), KRAS (p(HGNC:KRAS)) or CDC42 (p(HGNC:CDC42)).
gtpBoundActivity() represents the signaling activity of G-proteins, not GTPase Activity. GTPase activity catalyzes the hydrolysis of bound GTP to GDP, which leaves the G-protein inactive.

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kinaseActivity(), kin()

For the abundance term A, kinaseActivity(A) or kin(A) denotes the frequency or abundance of events in which a member of A acts as a kinase, performing enzymatic phosphorylation of a substrate via transfer of a phosphate group, usually from ATP. A should represent an abundance of protein or molecular complex with kinase activity, such as AKT1 (p(HGNC:AKT1)) or the AMP-activated protein kinase complex (complex(MC:"AMP-activated protein kinase complex")).

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molecularActivity(), act()

For the abundance term A, molecularActivity(A) or act(A) denotes the frequency or abundance of events in which a member of A acts as a causal agent at the molecular scale. The nature of the activity is unspecified.
This term function may be used to represent activities of molecular entities in cases where the mechanism of action the entity is unknown or is not represented by another activity function. For example, the toll-like receptor TLR4 does not have a specific enzymatic activity, but signal transduction downstream from TLR4 protein, such as that activated by TLR4 binding its ligand lipopolysaccharide, can be represented as molecularActivity(p(HGNC:TLR4)).

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peptidaseActivity(), pep()

For the abundance term A, peptidaseActivity(A) or pep(A) denotes the frequency or abundance of events in which a member of A acts to cleave a protein via hydrolysis of the peptide bonds that link amino acids together in the polypeptide chain forming the protein. A should represent an abundance of protein or molecular complex with peptidase activity, such as angiotensin-converting enzyme (p(HGNC:ACE)).

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phosphataseActivity(), phos()

For the abundance term A, phosphataseActivity(A) or phos(A) denotes the frequency or abundance of events in which a member of A acts as a phosphatase, performing enzymatic removal of a phosphate from a substrate; A should represent an abundance of a protein or molecular complex with phosphatase activity, such as PTEN (p(HGNC:PTEN)) or DUSP1 (p(HGNC:DUSP1)).

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ribosylationActivity(), ribo()

For the abundance term A, ribosylationActivity(A) or ribo(A) denotes the frequency or abundance of events in which a member of A acts as a ribosylase to perform post-translational modification of proteins via the addition of one or more ADP-ribose moieties; A should represent an abundance of protein or molecular complex with ribosylation activity, such as PARP1 (p(HGNC:PARP1)).

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transcriptionalActivity(), tscript()

For the abundance term A, transcriptionalActivity(A) or tscript(A) denotes the frequency or abundance of events in which a member of A directly acts to control transcription, the copying of DNA into RNA. A should represent the abundance of a protein or molecular complex with transcriptional activity, such as the glucocorticoid receptor (p(HGNC:NR3C1)) or the AP-1 transcription complex (complex(NCH:"AP-1 complex")).
Activities represented using this term function include the activities of abundances of proteins or molecular complexes that bind DNA directly and act as transcription factors, as well as transcriptional corepressors and coactivators which directly regulate transcription factor activity.

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transportActivity(), tport()

For the abundance term A, transportActivity(A) or tport(A) denotes the frequency or abundance of events in which a member of A directly acts to enable the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells. A should represent an abundance of protein or molecular complex with transporter activity, such as aquaporin 1 (p(HGNC:AQP1)), Scavenger receptor class B member 1 (p(HGNC:SCARB1)), or the epithelial sodium channel (ENaC) complex (complex(NCH:"ENAC complex")). This function only applies to cases involving movement of molecules at a cellular scale.