Batch Query Help

Curated chemical–gene interactions

Valid input to retrieve curated chemical–gene interactions are chemicals (names, synonyms, CAS RNs and MeSH IDs) and genes (NCBI symbols and 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 is qualified by a degree: increases, decreases, affects or does not affect (e.g., “Chemical X increases expression of Gene Y mRNA”). The affects degree is used when the reference does not describe a more specific degree. Interactions having the does not affect degree are excluded from our public data.

An interaction type must be selected in order to filter by degree(s). At least one degree must be checked.

Type. To select or deselect multiple interaction types, hold the Ctrl key (PC) or ⌘/Open-Apple/Command key (Mac) while clicking. Interaction types are searched in this 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.
— 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.
— 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).

Chemical associations

Valid inputs to retrieve curated chemical associations are genes (NCBI symbols and 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 curated and/or inferred associations with specified diseases. Curated chemical–disease associations are extracted from the published literature by CTD curators. Inferred associations 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 curated association with disease B).

Gene associations

Valid inputs to retrieve gene associations are chemicals (names, synonyms, CAS RNs and MeSH IDs), diseases (names, synonyms and MeSH or OMIM IDs), GO terms (accession IDs and names), and pathways (KEGG or REACTOME names or accession IDs).

Chemical input will retrieve genes involved in curated interactions with specified chemicals.

Disease input will retrieve genes involved in curated and/or inferred associations with specified diseases. Curated gene–disease associations are extracted from the published literature by CTD curators, or are derived from the OMIM database using the mim2gene file from the NCBI Gene database. Inferred associations 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 curated association with disease B).

GO term input will retrieve genes annotated to that GO term or one of its descendants.

Pathway input will retrieve genes annotated to that pathway by KEGG or REACTOME curation.

Disease associations

Valid inputs to retrieve disease associations are chemicals (names, synonyms, CAS RNs and MeSH IDs), genes (NCBI symbols and IDs), GO terms (accession IDs and names), and pathways (KEGG or REACTOME names or accession IDs).

Chemical input will retrieve diseases involved in curated and/or inferred associations. Curated chemical–disease associations are extracted from the published literature by CTD curators. Inferred associations 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 curated association with disease B).

Gene input will retrieve diseases involved in curated and/or inferred associations. Curated gene–disease associations are extracted from the published literature by CTD curators, or are derived from the OMIM database using the mim2gene file from the NCBI Gene database. Inferred associations 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 curated association with disease B).

GO term input will retrieve disease associations inferred between the input GO term or one of its descendants.

Disease input will retrieve disease associations inferred based on shared genes among CTD-curated gene–disease associations and gene–pathway associations established by KEGG and REACTOME curation.

Pathway associations

Valid inputs to retrieve pathway associations are chemicals (names, synonyms, CAS RNs and MeSH IDs), genes (NCBI symbols and 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. Alternatively, only those pathways found to be enriched significantly among genes that interact with a chemical may be retrieved. More…

Gene input will identify pathways involving these genes based on annotation from the KEGG and REACTOME databases.

Disease input will identify pathways inferred to be associated with these diseases based on shared genes among CTD-curated gene–disease associations and gene–pathway associations established by KEGG and and REACTOME curation.

Gene Ontology associations

Valid inputs to retrieve GO annotations are chemicals (names, synonyms, CAS RNs and MeSH IDs) and genes (NCBI symbols and IDs).

You must select one or more GO ontologies of interest (i.e., Biological Process, Molecular Function and/or Cellular Component).

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. Alternatively, only those GO terms found to be enriched significantly among genes that interact with a chemical may be retrieved. More…

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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