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Glossary

Contents

  1. Chemical–Gene Interaction Types
  2. Chemical–Disease Interaction Types
  3. Gene–Disease Interaction Types
  4. Evidence Codes

Top ↑ Chemical–Gene Interaction Types

CTD curates chemical–gene and –protein interactions in vertebrates and invertebrates using this hierarchical vocabulary of interaction types (download it):

abundance
The abundance of a chemical (if chemical synthesis is not known).
activity
An elemental function of a molecule.
binding
A molecular interaction.
cotreatment
Involving the use of two or more chemicals simultaneously.
expression
The expression of a gene product.
folding
The bending and positioning of a molecule to achieve conformational integrity.
localization
Part of the cell where a molecule resides.
metabolic processing
The biochemical alteration of a molecule's structure (does not include changes in expression, stability, folding, localization, splicing, or transport).
—  acetylation
The addition of an acetyl group.
—  acylation
The addition of an acyl group.
—  alkylation
The addition of an alkyl group.
—  amination
The addition of an amine group.
—  carbamoylation
The addition of a carbamoyl group.
—  carboxylation
The addition of a carboxyl group.
—  chemical synthesis
A biochemical event resulting in a new chemical product.
—  degradation
Catabolism or breakdown.
    —  cleavage
The processing or splitting of a molecule, not necessarily leading to the destruction of the molecule.
        —  hydrolysis
The splitting of a molecule via the specific use of water.
—  ethylation
The addition of an ethyl group.
—  glutathionylation
The addition of a glutathione group.
—  glycation
The non-enzymatic addition of a sugar.
—  glycosylation
The addition of a sugar group.
    —  glucuronidation
The addition of a sugar group to form a glucuronide, typically part of an inactivating or detoxifying reaction.
    —  N-linked glycosylation
The addition of a sugar group to an amide nitrogen.
    —  O-linked glycosylation
The addition of a sugar group to a hydroxyl group.
—  hydroxylation
The addition of a hydroxy group.
—  lipidation
The addition of a lipid group.
    —  farnesylation
The addition of a farnesyl group.
    —  geranoylation
The addition of a geranoyl group.
    —  myristoylation
The addition of a myristoyl group.
    —  palmitoylation
The addition of a palmitoyl group.
    —  prenylation
The addition of a prenyl group.
—  methylation
The addition of a methyl group.
—  nitrosation
The addition of a nitroso or nitrosyl group.
—  nucleotidylation
The addition of a nucleotidyl group.
—  oxidation
The loss of electrons.
—  phosphorylation
The addition of a phosphate group.
—  polymerization
The addition of extra monomers to form a polymer.
—  reduction
The gain of electrons.
—  ribosylation
The addition of a ribosyl group.
    —  ADP-ribosylation
The addition of a ADP-ribosyl group.
—  sulfation
The addition of a sulfate group.
—  sumoylation
The addition of a SUMO group.
—  ubiquitination
The addition of an ubiquitin group.
mutagenesis
The genetic alteration of a gene product.
reaction
Any general biochemical or molecular event.
response to substance
Resistance or sensitivity to a substance.
splicing
The removal of introns to generate mRNA.
stability
Overall molecular integrity.
transport
The movement of a molecule into or out of a cell.
—  secretion
The movement of a molecule out of a cell (by less specific means than export).
    —  export
The movement of a molecule out of a cell (by more specific means than secretion).
—  uptake
The movement of a molecule into a cell (by less specific means than import).
    —  import
The movement of a molecule into a cell (by more specific means than uptake).

Top ↑ Chemical–Disease Interaction Types

CTD uses this vocabulary of chemical–disease interaction types:

marker/mechanism
A chemical that correlates with a disease (e.g., increased abundance in the brain of chemical X correlates with Alzheimer disease) or may play a role in the etiology of a disease (e.g., exposure to chemical X causes lung cancer).
therapeutic
A chemical that has a known or potential therapeutic role in a disease (e.g., chemical X is used to treat leukemia).

Top ↑ Gene–Disease Interaction Types

CTD uses this vocabulary of gene–disease interaction types:

marker/mechanism
A gene that may be a biomarker of a disease (e.g., increased expression of gene X correlates with breast cancer) or play a role in the etiology of a disease (e.g., mutations in gene X causes liver cancer).
therapeutic
A gene that is or may be a therapeutic target in the treatment a disease (e.g., targeted reduction of gene X expression reduces susceptibility to emphysema).

Top ↑ Evidence Codes

CTD uses evidence codes developed by the Gene Ontology Consortium:

EXP
inferred from experiment.
HTP
high throughput.
IC
inferred by curator.
IDA
inferred from direct assay.
IEA
inferred from electronic annotation.
IEP
inferred from expression pattern.
IGI
inferred from genetic interaction.
IMP
inferred from mutant phenotype.
IPI
inferred from physical interaction.
ISA
inferred from sequence alignment.
ISM
inferred from sequence model.
ISO
inferred from sequence orthology.
ISS
inferred from sequence or structural similarity.
NAS
non-traceable author statement.
ND
no biological data available.
NR
not recorded.
RCA
inferred from reviewed computational analysis.
TAS
traceable author statement.