Batch Query Help

Select your input type

Select the type of the query terms you are providing in Step 2.

Chemicals

Retrieve data associated with the chemicals that you specify in Step 2. You may identify chemicals by MeSH^® name, synonym, or accession ID (“MESH:…”), or by CAS RN. To limit your search to official names, use the “name:” prefix.

Diseases

Retrieve data associated with the diseases that you specify in Step 2. You may identify diseases by MeSH or OMIM name, synonym, or accession ID (“MESH:…” or “OMIM:…”). To limit your search to official names, use the “name:” prefix.

Genes

Retrieve data associated with the genes that you specify in Step 2. You may identify genes by NCBI (Entrez Gene) symbols (“name:…”) or accession IDs (“GENE:…”).

Gene Ontology terms

Retrieve data associated with the GO terms that you specify in Step 2. You may identify GO terms by name, synonym, or ID (e.g., “GO:0008219” or “8219”).

Pathways

Retrieve data associated with the pathways that you specify in Step 2. You may identify pathways by KEGG or REACTOME name or accession ID (“KEGG:…” or “REACT:…”).

References

Retrieve data associated with the references that you specify in Step 2. You may identify references by PubMed^® IDs or DOIs.

Downloading chemical–gene interactions

Valid input to retrieve curated chemical–gene interactions are chemicals, genes, and references.

CTD chemical–gene and protein interactions are curated 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).

Downloading gene associations

Chemical inputs retrieve genes involved in curated interactions with specified chemicals.

Disease inputs 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).

Gene inputs retrieve associated gene/protein interactions.

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

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

Reference inputs retrieve genes involved in chemical interactions or disease associations curated from the specified references.

Downloading disease associations

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

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

Reference inputs retrieve chemical– and gene–disease associations curated from the specified references.

Illuminating how chemicals affect human health.
Comparative Toxicogenomics Database

Help: Batch Query

Contents

Overview

Batch Query API