Assigning Go Identifiers To Gsea Msigdb Gene Sets

Question

[nbartonicek]

I performed a GSEA analysis using the GO derived gene sets and would like to assign a GO id to the gene set names. Though the information is available set-by-set (http://www.broadinstitute.org/gsea/msigdb/cards/ACTINFILAMENTBASED_PROCESS.html), it would be great if there was a way to batch annotate the list.

There must be a tool to do this (biomaRt does not help).

Grateful for any information!

Cheers,

Nenad Bartonicek

PhD student, Enright group European Bioinformatics Institute Hinxton Cambridge CB10 1SD United Kingdom

Answer 1

[Sean Davis]

The simplest way may be to download the large XML file from the Broad site and use a small script in your language of choice to extract the GO id from the text description of the gene set.