Cool stuff Ensembl VEP can do: Using Gene Ontology annotations to understand gene function

Ensembl VEP maps your variants to genes but what do those genes do?

The Gene Ontology (GO) annotates genes with molecular function, the cellular location in which the gene product functions and the biological process in which the gene product is involved. In addition to phenotype association information, which is only available for a few genes, we now show GO annotations to help guide variant prioritisation by providing an indication of the functionality a variant may affect.

To enable GO annotations in the Ensembl VEP web interface , navigate to ‘Additional annotations’ section.

and select ‘Gene Ontology’ from the ‘Phenotype data and citations’ options – as shown:

You will then be able to view GO terms relative to each transcript with links to detailed information in QuickGO, as shown below (you will need to select GO terms using the Show/hide columns button).

GO annotations are available via the Ensembl VEP web interface for a range of vertebrate species including human, mouse, rat and major agricultural species. They are also available as an option in the Ensembl VEP REST API. GO annotations can be accessed for a wider range of species via a recently updated plugin for the command line version of Ensembl VEP,  enabling fast, local analysis behind your firewall.

Post written by Ensembl Variation and edited by Aleena Mushtaq