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Comparative Toxicogenomics Database

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Contents

1. Introduction
2. Chemical inputs
3. Disease inputs
4. Gene inputs
5. Gene associations
6. Chemical associations
7. Disease relationships
8. Pathway associations
9. Gene Ontology (GO) associations

Introduction

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 (“ID:#####”), 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 (“ID:#####”).

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 official symbols or accession IDs (“ID:#####”).

Gene associations

Select this option to compare genes with:

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

Chemical associations

Select this option to compare chemicals with:

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

Disease relationships

Select this option to compare direct or inferred diseases relationships with chemical or gene inputs. Direct relationships are established by CTD (chemical–disease and gene–disease) and OMIM (gene–disease) curation. Inferred relationships 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 direct relationship with Disease B).

Pathway associations

Select this option to compare annotated pathways for gene and disease inputs or inferred pathways for chemical inputs. Annotated pathways include gene–pathway and disease–pathway 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 and REACTOME curation.

Gene Ontology (GO) associations

Select this option to compare Gene Ontology (GO) associations for chemical and gene inputs. You must select your ontology of interest (i.e., biological processes, molecular functions or cellular components). Gene inputs return cross-species GO annotations for genes. Chemical inputs return cross-species GO annotations for genes with CTD-curated chemical interactions.