Chemical

The name or symbol of a chemical involved in an interaction. Synonyms are also matched.

Examples: dioxin, 1746-01-6, chemtreeno:D02.455.526.439.337

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.

You may 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 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).

Gene

The name, symbol or NCBI Gene accession ID of a gene or protein involved in an interaction. Synonyms are also matched.

To search by NCBI Gene accession ID, you must include “geneid:” before the accession number.

Examples: ahr, aryl hydrocarbon receptor

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 unselect multiple gene forms, press 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

KEGG and REACTOME pathway data is a collection of manually drawn pathway maps representing our knowledge on the 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.

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. You may 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 number. You may also select a KEGG or REACTOME pathway by clicking the Select button and navigating through the list.

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.

Examples: zebrafish, teleostei, taxonid: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.

You may 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

The GO vocabularies are hierarchical, so searches return terms that match your query exactly as well as more detailed terms.

You may 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. You may also select a GO ID by clicking the Select button and navigating through the hierarchy.

Results per page

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

Search

Click the Search button to submit your query.

Clear

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