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CTD curates specific chemical–gene and protein interactions in vertebrates and invertebrates from the published literature. Most interactions are binary, involving one chemical and one gene or protein (e.g., “3-methylquercetin results in decreased activity of ABCC1 protein”). Brackets represent nested events in more complex interactions (e.g., “[3,4,5,3',4'-pentachlorobiphenyl binds to AHR protein] which results in increased expression of ABCC3 mRNA”).
The chemical–gene interaction query may be used to retrieve cross-species chemical–gene and protein interactions curated from the published literature.
You must specify at least one chemical, gene, organism or GO term to perform a query.
See also: Advanced Queries.
The name, symbol, CAS Registry Number, or MeSH accession ID (prefixed with “MESH:”) of a chemical involved in an interaction. Synonyms are also matched. To limit your search to official names, use the “name:” prefix.
Examples: dioxin, name:mercury, 1746-01-6, MESH:D001151
CTD's chemical vocabulary consists of a subset of the Medical Subject Headings (MeSH®), the hierarchical vocabulary from the U.S. National Library of Medicine. More…
The chemical vocabulary is hierarchical, so you may search by a narrow (e.g., “copper”) or broad term (e.g., “heavy metals”). Queries that use broad terms retrieve results matching the broad terms as well as related, more specific terms.
Enter your query term in the open field or choose a term from the hierarchical vocabulary by clicking the Select button and navigating through the tree.
CTD curates specific chemical–gene and –protein interactions in vertebrates and invertebrates from published references. You may search for specific types of interactions by selecting a term or terms in this field. Each interaction has a degree and type as defined 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:
The name, symbol or NCBI Gene accession ID (prefixed with “GENE:”) of a gene or protein involved in an interaction. Synonyms are also matched. To limit your search to official symbols, use the “name:” prefix.
Examples: ahr, name:brca1, aryl hydrocarbon receptor, GENE:196
The cross-species gene vocabulary (symbols, names, and synonyms) in CTD is derived from the Gene database at the National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine. CTD curators may add to this vocabulary as required (e.g., to represent a species-specific gene that is not curated in NCBI Gene).
Each curated chemical–gene interaction includes the form of the gene that is involved (e.g., promoter, mRNA, protein). Gene forms may be specified when searching for curated interaction data.
An interaction type must be selected in order to specify gene forms.
To select or deselect multiple gene forms, hold the Ctrl key (PC) or ⌘/Open-Apple/Command key (Mac) while clicking. Gene forms are searched in the hierarchy shown on the query form.
You may search for chemical–gene interactions by pathway. Results will comprise interactions involving a gene or protein that also functions in a KEGG or REACTOME pathway. Enter either the name of the pathway (“Alzheimer’s disease”) or the KEGG or REACTOME ID of the term. To search by KEGG or REACTOME ID, you must include “KEGG:” or “REACT:”, respectively, before the accession ID. You may also select a pathway by clicking the Select button and navigating through the list.
KEGG and REACTOME pathway data describe known molecular interaction and reaction networks. These data are integrated with chemicals, genes, and diseases in CTD to provide insights into molecular networks that may be affected by chemicals, and possible mechanisms underlying environmental diseases.
The common or scientific name of an organism or a higher-order taxon in which a curated chemical–gene or protein interaction was reported. To limit your search to official scientific names, use the “name:” prefix.
Examples: zebrafish, name:homo sapiens, felis catus, TAXON:9685
CTD's organism vocabulary consists of the Eumetazoa (vertebrates and invertebrates) component of the Taxonomy Database from NCBI, a division of the U.S. National Library of Medicine. The vocabulary is hierarchical, so you may search by a specific organism (e.g., “homo sapiens”) or a higher-order taxon (e.g., “mammalia”). A query that uses a higher-order taxon will retrieve results that match that taxon as well as the more specific taxa included within it.
Enter your query term in the open field or choose a term from the hierarchical vocabulary by clicking the Select button and navigating through the tree.
The molecular function, biological process, or cellular component annotated to the sequences of a protein involved in an interaction.
Examples: nucleotide binding, GO:0006915, name:anti-apoptosis
The GO ontologies are hierarchical, so searches return terms that match your query exactly as well as more detailed terms.
Enter either the name or a synonym of the term or the GO ID of the term (e.g., “GO:0006915”). To search by GO ID, you must include “go:” before the accession number. To limit your search to official names, use the “name:” prefix. You may also select a term by clicking the Select button and navigating through the hierarchy.
Select the primary sorting order of the results:
The number of results displayed per page. A lower number provides faster response.
Click the Search button to submit your query.
Click the Clear button to clear and reset all fields to their default values.
Interaction query results are presented in a tabular format that shows the interacting genes and chemicals, organism, and reporting reference for each interaction. A single interaction may be represented several times in this table: once for each unique combination of chemical, gene, and reference.
From results pages, you may access detail pages about the interacting genes and chemicals, organisms, and references.
The name of an interacting chemical in the interaction. Click the chemical name to view the chemical's detail page.
The symbol of an interacting gene in the interaction. Click the gene symbol to view the gene's detail page.
The description of the interaction.
Action degrees are color-coded by category:
The number of references reporting the interaction. Click to view the reporting references and organisms.
The number of organisms in which the interaction was reported and which match the current query. Click to view the reporting references and organisms.
Sort these data differently by clicking a column heading.
Save these data into a comma-separated values (CSV), Excel, XML, or tab-separated values (TSV) file by clicking a Download link at the bottom of the table.