======================================
How to use MsigDB gene-sets in Gitools
======================================

The Molecular Signatures Database (  `MSigDB <http://www.broadinstitute.org/gsea/msigdb/>`_ ) contains an extensive
collection of gene sets that can be downloaded and used in Gitools. To do that follow these steps:

 #. Go to  `Downloads in MSigDB <http://www.broadinstitute.org/gsea/downloads.jsp#msigdb>`_
 #. You will have to login (or register if this is your first time in MSigDB)
 #. You will see a list of links to download different collections of gene sets.
 #. Click the collection you are interested to download. **Download in gmt format**, this is the format the Gitools understand.
 #. You can download the gene sets with different gene ids (eg. symbol or entrez), you should use the same gene id as you have in your data.
 #. Save the gmt file in your computer and it is ready to be used in an :doc:`Enrichment Analysis in Gitools <UserGuide_Enrichment>` .
