Enrichment Plot

[Theresa B]

Hello!

I've noticed in publications how smooth enrichment plots can be and was wondering if I've done something incorrectly with mine. I've attached an example. The proteins being used are from EVs and are the 2-peptide containing protein list. 

[Anthony Castanza]

Hi Theresa,

The enrichment plots which you saw elsewhere were likely from whole transcriptome expression studies which have a much fuller picture of the gene landscape and are really what the intended use-case is for GSEA. GSEA can be used with other data types but we can't really vouch for the results. One of the biggest caveats that you should be aware of is that  GSEA can only analyze the gene universe that is present in your study so if a gene set contains several hundred genes but only 15 of them are present in your study, GSEA will treat that set as if it only has those 15 genes which can cause significant amounts of information to be lost. So when running very small ranked lists like this it is important to ensure that any result sets are still representative of their original annotations.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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