Giving insight into how chemicals affect our health.
Comparative Toxicogenomics Database

Contents

1. Overview
2. Chemical inputs
3. Disease inputs
4. Gene inputs
5. Chemical associations
6. Gene associations
7. Disease associations
8. Pathway associations
9. Gene Ontology associations
10. Filter: disease interaction type

Overview

The VennViewer tool allows you to generate a Venn diagram that will identify logical relationships between data sets in CTD that are associated with two or three chemicals, genes or diseases.

Chemical inputs

Select this option to compare associated data sets of two or three chemicals that you specify in Step 2. You may specify chemicals by MeSH^® name, synonym or accession ID (“MESH:#####”), or by CAS RN.

Disease inputs

Select this option to compare associated data sets of two or three diseases that you specify in Step 2. You may specify diseases by MeSH or OMIM name, synonym or accession ID (“MESH:#####” or “OMIM:#####”).

Gene inputs

Select this option to compare associated data sets of two or three genes that you specify in Step 2. You may specify genes by NCBI symbols or accession IDs (“GENE:#####”).

Chemical associations

Select this option to compare chemicals with:

• curated interactions with gene inputs,
• curated associations with disease inputs, or
• inferred associations with disease inputs. Inferred chemical associations are established via curated disease–gene associations and gene–chemical interactions (e.g., Disease A has a curated association with Gene B and Gene B has a curated interaction with Chemical C).

Gene associations

Select this option to compare genes with:

• curated interactions with chemical inputs,
• curated associations with disease inputs, or
• inferred associations with disease inputs. Inferred gene associations are established via curated disease–chemical associations and chemical–gene interactions (e.g., Disease A has a curated association with Chemical B and Chemical B has a curated interaction with Gene C).

Disease associations

Select this option to compare curated or inferred diseases associations with chemical or gene inputs. Curated associations are established by CTD (chemical–disease and gene–disease) and OMIM (gene–disease) curation. 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).

Pathway associations

Select this option to compare annotated pathways for gene inputs, inferred pathways for disease inputs, or inferred or enriched pathways for chemical inputs.

Annotated pathways for genes are associations established by KEGG and REACTOME curation.

Inferred pathways for chemicals are based on CTD-curated chemical–gene interactions and gene–pathway associations established by KEGG and REACTOME curation. Alternatively, only those pathways found to be enriched significantly among genes that interact with the chemical may be retrieved. More…

Inferred pathways for diseases are based on shared genes among CTD-curated gene–disease associations and gene–pathway associations established by KEGG and REACTOME curation.

Gene Ontology associations

Select this option to compare Gene Ontology (GO) associations for chemical and gene inputs.You must also select your GO ontology of interest (i.e., Biological Process, Molecular Function or Cellular Component).

Gene inputs return cross-species GO annotations for genes.

Chemical inputs return cross-species GO annotations for genes with CTD-curated chemical interactions. Alternatively, only those GO terms found to be enriched significantly among genes that interact with the chemical may be retrieved. More…

Filter: disease interaction type

Curated chemical–disease and gene–disease data sets may be filtered by their interaction types.