import-export selected gene sets in GSEA
Mohsen Fathzadeh
I have exported a list of 11 gene sets as .gmt and do not know how to import this file into GSEA for analysis.
If I understood correctly, I need to install another application known as MSigDB XML Browser application to enable this feature.
Unfortuenly, I am not skillful with coding in MAC Terminal to install java 11 and/or could not troubleshoot/launch the MSigDB application.
Any thoughts, feedback, and resources that help me through this would greatly be appreciated.
Thanks,
Mohsen
Anthony Castanza
Hi Mohsen,
If you’ve already retrieved the gene sets as GMT files, you can load them in through the Load data panel in GSEA the same way you load in datasets. You do not need the XML browser.
Once you’ve loaded in the gene sets, they should appear in the “Gene matrix (local gmx/gmt)” tab in the Gene sets database dialogue.
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
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