Contents

  1. Overview
  2. Input type
  3. Output data sets
  4. Filters

Overview

The VennViewer tool allows you to generate Venn diagrams to illustrate logical relationships among data sets that are associated with two or three chemicals, genes, or diseases.

Input type

Chemicals

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. To limit your search to official names, use the “name:” prefix.

Diseases

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:…”). To limit your search to official names, use the “name:” prefix.

Genes

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 (Entrez Gene) symbols or accession IDs (“GENE:…”).

Output data sets

Chemical associations

Select this report to compare chemicals with:

Gene associations

Select this report to compare genes with:

Disease associations

Select this report 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 report 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 report to compare Gene Ontology (GO) associations for chemical and gene inputs. You must also select your 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…

Filters

Chemical–gene interaction type

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

Disease interaction type

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