Reaction Effects Described in TRANSPATH

Reaction effects described in TRANSPATH are defined in the table below, with links to some examples of reactions that include these effects.

TRANSPATH Reaction Effect Terms and Their Meanings

Effect	Related TP Effect Term	Definition
Abundance	Decrease in abundance	Abundance of a protein is decreased by an indirect mechanism.
	Increase in abundance	Abundance of a protein is increased by an indirect mechanism.
	Regulation of abundance	Abundance of a protein is altered in an unspecified manner.
Acetylation	Acetylation	Posttranslational protein modification, whereby one or more acetyl groups are attached, generally at the N-terminus.
	Deacetylation	The removal of an acetyl group.
	Decrease in acetylation	Acetylation of a protein is decreased by an indirect mechanism.
	Increase in acetylation	Acetylation of a protein is increased by an indirect mechanism.
	Regulation of acetylation	Acetylation of a protein is altered in an unspecified manner.
Activity	Activation	Increase in protein activity; reactions going out from the target molecule continue after this reaction.
	Inhibition	Decrease in protein activity; reactions going out from the target molecule will not continue after this reaction.
	Regulation of activity	Activity of a protein is altered in an unspecified manner.
	Unknown	Used for semantic reactions where its unclear if the signal acceptor is activated or inhibited.
Acylation	Acylation	Process of adding an acyl group to a compound.
	Deacylation	The removal of an acyl group.
	Decrease in acylation	Acylation of a protein is decreased by an indirect mechanism.
	Increase in acylation	Acylation of a protein is increased by an indirect mechanism.
	Regulation of acylation	Acylation of a protein is altered in an unspecified manner.
ADP-ribosylation	ADP-ribosylation	The transfer of ADP-ribose from NAD to a protein amino acid.¹.
	Decrease in ADP-ribosylation	ADP-ribosylation of a protein is decreased by an indirect mechanism.
	Increase in ADP-ribosylation	ADP-ribosylation of a protein is increased by an indirect mechanism.
Amidation	Amidation	The addition of an amide group from glycine to a protein amino acid.¹
	Deamidation	The removal of an amide group.
	Decrease in amidation	Amidation of a protein is decreased by an indirect mechanism.
	Increase in amidation	Amidation of a protein is increased by an indirect mechanism.
	Regulation of amidation	Amidation of a protein is altered in an unspecified manner.
Assembly of complexes	Oligomerization	Assembly of a complex; includes homodimer, heterodimer, homotrimer, heterotrimer...etc.
	Dissociation	Breakup of a complex.
	Decrease in oligomerization	Oligomerization of a protein to binding partners is decreased by an indirect mechanism.
	Increase in oligomerization	Oligomerization of a protein to binding partners is increased by an indirect mechanism.
Assembly of molecules	Assembly	The congregation of molecules in a particular subcellular location (membranous lipid rafts, for example).
Automodification	Automodification	A protein modification reaction where the enzyme is also the substrate; this effect term should be used together with a specific modification term (phosphorylation, for example).
Binding	Binding	Describes any type of chemical/physical bond (covalent bond, hydrogen bond, ion complex, Van-der-Waals) that is established between reaction partners, if not defined more specifically as condensation, acetylation... etc.
	Decrease in binding	Binding of a protein to a molecule is decreased by an indirect mechanism.
	Increase in binding	Binding of a protein to a molecule is increased by an indirect mechanism.
Carboxylation	Carboxylation	The addition of a carboxy group to a protein amino acid.¹
	Decarboxylation	The removal of a carboxyl group.
	Decrease in carboxylation	Carboxylation of a protein is decreased by an indirect mechanism.
	Increase in carboxylation	Carboxylation of a protein is increased by an indirect mechanism.
	Regulation of carboxylation	Carboxylation of a protein is altered in an unspecified manner.
Cholesterol modification	Cholesterol modification
	Decrease in cholesterol modification
	Increase in cholesterol modification
Cleavage	Cleavage	The hydrolysis of a peptide bond by an endoprotease.
	Decrease in cleavage	Cleavage of a protein is decreased by an indirect mechanism.
	Increase in cleavage	Cleavage of a protein is increased by an indirect mechanism.
	Regulation of cleavage	Cleavage of a protein is altered in an unspecified manner.
Competition	Competition	Describes two or more molecules competing for a reaction partner or signal.
Condensation	Condensation
Conjugation	Conjugation	The coupling of a molecule with one or more ubiquitin-like molecules.
	Deconjugation
	Decrease in conjugation	Conjugation of a protein is decreased by an indirect mechanism.
	Increase in conjugation	Conjugation of a protein is increased by an indirect mechanism.
Degradation	Degradation	Enzymatic breakdown of protein molecules, leaving behind protein remnants.
Demethylimination	Demethylimination	Conversion of a methylated arginine residue to citrulline.
DNA binding	DNA binding	Binding of a protein to the promoter/enhancer of a gene.
	Decrease in DNA binding	DNA binding of a protein is decreased by an indirect mechanism.
	Increase in DNA binding	DNA binding of a protein is increased by an indirect mechanism.
Exchange	Exchange	Catalyzed replacement of a group by another (exchange of G-protein associated GDP with GTP, catalyzed by a GEF, for example).
Expression	Expression	Transfer of information encoded in the DNA (nucleotide sequence) into the protein (amino acid sequence); reactions with effect expression include several steps: transcription, splicing, capping, and translation.
Folding	Decrease in folding	Folding of a protein is decreased by an indirect mechanism.
	Increase in Folding	Folding of a protein is increased by an indirect mechanism.
	Regulation of Folding	Folding of a protein is altered in an unspecified manner.
Glycosylation (also see N-glycosylation, O-glycosylation)	Glycosylation	Posttranslation modification of a protein, whereby glycosyl groups are transferred to certain amino acid residues.
	Deglycosylation	The removal of a glycosyl group.
	Decrease in glycosylation	Glycosylation of a protein is decreased by an indirect mechanism.
	Increase in glycosylation	Glycosylation of a protein is increased by an indirect mechanism.
	Regulation of glycosylation	Glycosylation of a protein is altered in an unspecified manner.
Hydrolysis	Hydrolysis	Catalyzed splitting of a chemical bond with the consumption of water.
Hydroxylation	Hydroxylation	Any chemical process that introduces one or more hydroxyl groups (-OH) into a compound (or radical), thereby oxidizing it.
	Dehydroxylation	Removal of a hydroxyl group.
	Decrease in hydroxylation	Hydroxylation of a protein is decreased by an indirect mechanism.
	Increase in hydroxylation	Hydroxylation of a protein is increased by an indirect mechanism.
Interaction	Interaction	Binary relationship that implies nothing about the directionality between two molecules or the mechanism of their interaction; both molecules are entered in the "molecules upstream" list.
Isomerization	Isomerization	Directed change between cis- and trans-conformation of a peptide chain.
	Decrease in isomerization	Isomerization of a protein is decreased by an indirect mechanism.
	Increase in isomerization	Isomerization of a protein is increased by an indirect mechanism.
Methylation	Methylation	Posttranslational modification of a protein that involves covalent transfer of a methyl-group to a substrate.
	Demethylation	The removal of a methyl group.
	Decrease in methylation	Methylation of a protein is decreased by an indirect mechanism.
	Increase in methylation	Methylation of a protein is increased by an indirect mechanism.
	Regulation of methylation	Methylation of a protein is altered in an unspecified manner.
mRNA decay	Increase in mRNA decay	miRNA triggered increase of target mRNA decay, thereby inhibiting translation.
Myristoylation	Myristoylation	Covalent or non-covalent attachment of a myristoyl moiety to a protein amino acid.¹
	Demyristoylation	The removal of a myristoyl moiety.
	Decrease in myristoylation	Myristoylation of a protein is decreased by an indirect mechanism.
	Increase in myristoylation	Myristoylation of a protein is increased by an indirect mechanism.
Neddylation	Neddylation	Specific conjugation such as ubiquitination or sumoylation; NEDD8, the mammalian homolog of Rub1, can likewise become covalently linked.
	Deneddylation	The removal one or more NEDD8 moieties from a protein.
	Decrease in neddylation	Neddylation of a protein is decreased by an indirect mechanism.
	Increase in neddylation	Neddylation of a protein is increased by an indirect mechanism.
N-glycosylation	N-glycosylation	Posttranslation modification of a protein, whereby glycosyl groups are transferred to asparagine residues in the correct consensus sequence.
	Deglycosylation	The removal of a glycosyl group.
	Decrease in N-glycosylation	N-glycosylation of a protein is decreased by an indirect mechanism.
	Increase in N-glycosylation	N-glycosylation of a protein is increased by an indirect mechanism.
	Regulation of N-glycosylation	N-glycosylation of a protein is altered in an unspecified manner.
Nitration	Nitration
	Denitration
	Decrease in nitration	Nitration status of a protein is decreased by an indirect mechanism.
	Increase in nitration	Nitration status of a protein is increased by an indirect mechanism.
	Regulation of nitration	Nitration status of a protein is altered in an unspecified manner.
Nitrosylation	Nitrosylation	Covalent transfer of NO to a substrate; S-nitrosylation (transfer of NO to Cys-residues) of a protein controls its activity similar to O-phosphorylation.
	Denitrosylation
	Decrease in nitrosylation	Nitrosylation status of a protein is decreased by an indirect mechanism.
	Increase in nitrosylation	Nitrosylation status of a protein is increased by an indirect mechanism.
O-glycosylation	O-glycosylation	Posttranslation modification of a protein, whereby glycosyl groups are transferred to the hydroxyl group of serine, threonine, hydroxylysine, or hydroxyproline residues, or to the phenol group of tyrosine residues.
	Deglycosylation	The removal of a glycosyl group.
	Decrease in O-glycosylation	O-glycosylation of a protein is decreased by an indirect mechanism.
	Increase in O-glycosylation	O-glycosylation of a protein is increased by an indirect mechanism.
Oxidation-reduction	Redox reaction	Oxidation-reduction; a reaction in which one or more electrons are transferred.
Oxidation-reduction	Regulation of oxidation	Oxidation status of a protein is altered in an unspecified manner.
Palmitoylation	Palmitoylation	Covalent or non-covalent attachment of a palmitoyl moiety to a protein amino acid.¹
	Depalmitoylation	The removal of a palmitoyl moiety.
	Decrease in palmitoylation	Palmitoylation of a protein is decreased by an indirect mechanism.
	Increase in palmitoylation	Palmitoylation of a protein is increased by an indirect mechanism.
Phosphorylation	Phosphorylation	Catalyzed binding of a phosphate group to a molecule; mediated by protein kinases.
	Dephosphorylation	Catalyzed removal of a phosphate group from a molecule; mediated by phosphatases.
	Decrease in phosphorylation	Phosphorylation of a protein is decreased by an indirect mechanism; can occur via dephosphorylation or inhibition of phosphorylation.
	Increase in phosphorylation	Phosphorylation of a protein is increased by an indirect mechanism.
	Regulation of phosphorylation	Phosphorylation status of a protein is regulated in an undefined way.
Predicted	Predicted	in silico predicted interaction of a miRNA with a complementary site of a target mRNA.
Prenylation (includes farnesylation, (geranyl)geranylation)	Prenylation	Class of lipid modification involving covalent addition of either farnesyl (15-carbon) or geranylgeranyl (20-carbon) isoprenoids to conserved cysteine residues at or near the C-terminus of proteins.²
Processing	Processing	Catalyzed maturation of proteins (usually associated with proteolytic cutting of the signal peptide or more).
	Decrease in processing	Processing of a protein is decreased by an indirect mechanism.
	Increase in processing	Processing of a protein is increased by an indirect mechanism.
	Regulation of processing	Processing of a protein is regulated in an undefined way.
Secretion	Decrease in secretion	Secretion of a protein is decreased by an indirect mechanism.
	Increase in secretion	Secretion of a protein is increased by an indirect mechanism.
	Regulation of secretion	Secretion of a protein is altered in an unspecified manner.
Stability	Stabilization	Additional association of a protein enhances the stability of an already existing complex.
	Destabilization	Additional association of a protein decreases the stability/affinity of an existing complex.
	Regulation of stability	Stability of a protein is altered in an unspecified manner.
Sulfation	Sulfation	Catalyzed transfer of sulfate from PAPS (adenosine 3'-phosphate 5'-phosphosulfate) to the hydroxyl group of a peptidyltyrosine residue to form a tyrosine O4-sulfate ester and 3',5'-ADP.
	Desulfation	Removal of a sulfate group.
	Regulation of sulfation	Sulfation of a protein is altered in an unspecified manner.
Sumoylation	Sumoylation	Process by which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.¹
	Desumoylation	The removal of one or more SUMO moieties from a protein.
	Decrease in sumoylation	Sumoylation of a protein is decreased by an indirect mechanism.
	Increase in sumoylation	Sumoylation of a protein is increased by an indirect mechanism.
Translation	Translational repression	Repression of translation by an miRNA.
Translocation	Translocation	Regulated transfer of a signaling molecule to another subcellular location (often from the cytosol to the nucleus).
Transport	Decrease in Transport	Transport of a protein is decreased by an indirect mechanism.
	Increase in Transport	Transport of a protein is increased by an indirect mechanism.
	Regulation of Transport	Transport of a protein is altered in an unspecified manner.
Transregulation	Transregulation	Transcriptional regulation by binding of a transcription factor to its cognate site within the gene regulatory region; the term transregulation does not differentiate between activation or inhibition.
	Transactivation	General term for gene activation, involves transcription.
	Transrepression	Repression of a gene by a transcription factor.
Ubiquitination	Ubiquitination	Coupling of a molecule with ubiquitin.
	Deubiquitination	The removal of one or more ubiquitin moieties from a protein¹.
	Decrease in ubiquitination	Ubiquitination of a protein is decreased by an indirect mechanism.
	Increase in ubiquitination	Ubiquitination of a protein is increased by an indirect mechanism.
	Regulation of ubiquitination	Ubiquitination of a protein is altered in an unspecified manner.

References for Definitions

¹Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium, Nature Genet 25:25-29. [Abstract]

²Zhang FL, Casey PJ. (1996) Protein prenylation: molecular mechanisms and functional consequences, Annu Rev Biochem 65:241-269. [Abstract]