The Molecular Signatures Database ( 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
- 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 Enrichment Analysis in Gitools .