Chemical–Gene Interaction Types
CTD curates chemical–gene and –protein interactions in vertebrates and invertebrates using this
hierarchical vocabulary of interaction types
- The abundance of a chemical (if chemical synthesis is not known).
- An elemental function of a molecule.
- A molecular interaction.
- Involving the use of two or more chemicals simultaneously.
- The expression of a gene product.
- The bending and positioning of a molecule to achieve conformational integrity.
- Part of the cell where a molecule resides.
- The biochemical alteration of a molecule's structure (does not include changes in expression, stability, folding, localization, splicing, or transport).
- The addition of an acetyl group.
- The addition of an acyl group.
- The addition of an alkyl group.
- The addition of an amine group.
- The addition of a carbamoyl group.
- The addition of a carboxyl group.
- A biochemical event resulting in a new chemical product.
- Catabolism or breakdown.
- The processing or splitting of a molecule, not necessarily leading to the destruction of the molecule.
- The splitting of a molecule via the specific use of water.
- The addition of an ethyl group.
- The addition of a glutathione group.
- The non-enzymatic addition of a sugar.
- The addition of a sugar group.
- The addition of a sugar group to form a glucuronide, typically part of an inactivating or detoxifying reaction.
- The addition of a sugar group to an amide nitrogen.
- The addition of a sugar group to a hydroxyl group.
- The addition of a hydroxy group.
- The addition of a lipid group.
- The addition of a farnesyl group.
- The addition of a geranoyl group.
- The addition of a myristoyl group.
- The addition of a palmitoyl group.
- The addition of a prenyl group.
- The addition of a methyl group.
- The addition of a nitroso or nitrosyl group.
- The addition of a nucleotidyl group.
- The loss of electrons.
- The addition of a phosphate group.
- The gain of electrons.
- The addition of a ribosyl group.
- The addition of a ADP-ribosyl group.
- The addition of a sulfate group.
- The addition of a SUMO group.
- The addition of an ubiquitin group.
- The genetic alteration of a gene product.
- Any general biochemical or molecular event.
response to substance
- Resistance or sensitivity to a substance.
- The removal of introns to generate mRNA.
- Overall molecular integrity.
- The movement of a molecule into or out of a cell.
- The movement of a molecule out of a cell (by less specific means than export).
- The movement of a molecule out of a cell (by more specific means than secretion).
- The movement of a molecule into a cell (by less specific means than import).
- The movement of a molecule into a cell (by more specific means than uptake).
Chemical–Disease Interaction Types
CTD uses this vocabulary of chemical–disease interaction types:
- 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).
- A chemical that has a known or potential therapeutic role in a disease (e.g., chemical X is used to treat leukemia).
Gene–Disease Interaction Types
CTD uses this vocabulary of gene–disease interaction types:
- 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).
- 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).
CTD uses evidence codes developed by the Gene Ontology Consortium:
- inferred from experiment.
- high throughput.
- inferred by curator.
- inferred from direct assay.
- inferred from electronic annotation.
- inferred from expression pattern.
- inferred from genetic interaction.
- inferred from mutant phenotype.
- inferred from physical interaction.
- inferred from sequence alignment.
- inferred from sequence model.
- inferred from sequence orthology.
- inferred from sequence or structural similarity.
- non-traceable author statement.
- no biological data available.
- not recorded.
- inferred from reviewed computational analysis.
- traceable author statement.