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Help: Advanced Chemical–Gene Interaction Query

Contents

  1. Overview
  2. Query Fields
  3. Results

Overview

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.

Top ↑ Query Fields

Chemical

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.

Chemical–gene interaction

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:

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).

Gene

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).

Gene form

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.

Pathway

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.

Organism

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.

Gene Ontology

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.

Sort by

Select the primary sorting order of the results:

  • chemical name,
  • gene symbol,
  • interaction prose,
  • reference count, or
  • organism count

Results per page

The number of results displayed per page. A lower number provides faster response.

Clear

Click the Clear button to clear and reset all fields to their default values.

Top ↑ Results

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.

Interacting Chemical

The name of an interacting chemical in the interaction. Click the chemical name to view the chemical's detail page.

Interacting Gene

The symbol of an interacting gene in the interaction. Click the gene symbol to view the gene's detail page.

Interaction

The description of the interaction.

Action degrees are color-coded by category:

  • increases
  • decreases
  • affects (degree unspecified)

References

The number of references reporting the interaction. Click to view the reporting references and organisms.

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.

Sorting

Sort these data differently by clicking a column heading.

Download

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.