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Contents

  1. Curated chemical–gene interactions
  2. Curated chemical associations
  3. Curated gene associations
  4. Disease Relationships
  5. Gene Ontology (GO) associations
  6. Pathway associations

Curated chemical–gene interactions

Valid input to retrieve manually curated chemical–gene interactions are chemicals (names, synonyms, CAS RNs and MeSH IDs) and genes (official symbols and NCBI IDs). CTD chemical–gene and protein interactions are curated for CTD in vertebrates and invertebrates from the published literature. Interactions may be direct (e.g., “chemical binds to protein”) or indirect (e.g., “chemical results in increased phosphorylation of a protein” via intermediate events).

You may select one or more interaction types to filter the interactions in your results. ANY is the default selection and does not cause any items to be filtered out. Definitions of each term are provided below.

Degree. Each chemical–gene interaction curated for CTD is qualified by one of 4 possible degrees: increases, decreases, affects or does not affect (e.g., chemical X increases expression of gene Y mRNA). The degree affects is used when the reference does not describe a more specific degree.

An interaction type must be selected in order to specify a degree. At least one degree must be checked when a type is selected.

Type. To select or unselect multiple interaction types, press the Ctrl key (PC) or ⌘/Open-Apple/Command key (Mac) while clicking. Interaction types are searchable in the following hierarchy:

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.
    —  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.
    —  glucuronidation
The addition of a sugar group to form a glucuronide, typically part of an inactivating or detoxifying reaction.
—  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.
—  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 chemical
Chemical resistance or chemical sensitivity.
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).

Curated chemical associations

Valid inputs to retrieve manually curated chemical associations are genes (official symbols and NCBI IDs) and diseases (names, synonyms and MeSH or OMIM IDs). Gene input will retrieve chemicals involved in curated interactions with specified genes. Disease input will retrieve chemicals involved in direct or inferred relationships with specified diseases. Direct chemical–disease relationships are curated from the published literature by CTD curators. Inferred relationships are established via CTD-curated chemical–gene interactions (e.g., chemical A is associated with disease B because chemical A has a curated interaction with gene C, and gene C has a direct relationship with disease B).

Curated gene associations

Valid inputs to retrieve manually curated gene associations are chemicals (names, synonyms, CAS RNs and MeSH IDs) and diseases (names, synonyms and MeSH or OMIM IDs). Chemical input will retrieve genes involved in curated interactions with specified chemicals. Disease input will retrieve genes involved in direct or inferred relationships with specified diseases. Direct gene–disease relationships are curated from the published literature by CTD curators, or are derived from the OMIM database using the mim2gene file from the NCBI Gene database. Inferred relationships are established via CTD-curated chemical–gene interactions (e.g., gene A is associated with disease B because gene A has a curated interaction with chemical C, and chemical C has a direct relationship with disease B).

Pathway associations

Valid inputs to retrieve pathway associations are chemicals (names, synonyms, CAS RNs and MeSH IDs), genes (official symbols and NCBI IDs) and diseases (names, synonyms and MeSH or OMIM IDs). Chemical input will identify genes involved in curated interactions and retrieve pathways containing these genes. Gene input will identify pathways involving these genes based on annotation from the KEGG and REACTOME databases. Disease input will identify pathways associated with these diseases based on KEGG and REACTOME annotation.

Disease relationships

Valid inputs to retrieve disease associations are chemicals (names, synonyms, CAS RNs and MeSH IDs) and genes (official symbols and NCBI IDs). Chemical input will retrieve diseases involved in direct and/or inferred relationships. Direct chemical–disease relationships are curated from the published literature by CTD curators. Inferred relationships are established via CTD-curated chemical–gene interactions (e.g., chemical A is associated with disease B because chemical A has a curated interaction with gene C, and gene C has a direct relationship with disease B).

Gene input will retrieve diseases involved in direct and/or inferred relationships. Direct gene–disease relationships are curated from the published literature by CTD curators, or are derived from the OMIM database using the mim2gene file from the NCBI Gene database. Inferred relationships are established via CTD-curated chemical–gene interactions (e.g., gene A is associated with disease B because gene A has a curated interaction with chemical C, and chemical C has a direct relationship with disease B).

Gene Ontology (GO) associations

Valid inputs to retrieve GO annotations are chemicals (names, synonyms, CAS RNs and MeSH IDs) and genes (official symbols and NCBI IDs). Chemical input will identify genes involved in curated interactions and retrieve a cross–species summary of GO terms used to annotate any of the UniProt (Swiss-Prot/TrEMBL) sequences encoded by these genes. Gene input will retrieve a cross–species summary of GO terms used to annotate any of the UniProt (Swiss-Prot/TrEMBL) sequences encoded by specified genes.

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