GSEA Preranked Assuming gene-gene expression independence

[Alex Lorenzo Starr]

Hello,

I have been using GSEA Preranked to try to test for enrichments in my data.  However, there are very few terms that beat an FDR of 0.1 (or even 0.25).  My situation is somewhat unique in that I am able to assume that there are no correlations between the expression of different genes.  I was wondering: do you have any suggestions on how to conduct enrichment analysis of a preranked list of genes assuming independence of gene-gene expression to improve sensitivity?  I have tried GOrilla, but it only works with gene ontology (as their code is not, to my knowledge, publicly available) and I would like to be able to apply this method to other gene sets.  Thanks in advance!

Best, Alex.

[Anthony Castanza]

Hi Alex,

 

I'm really not sure how to help you here. We don’t provide support for Gorilla as it isn't our software and I don't know anything more about its algorithm than you do. GSEA is capable of performing enrichment analysis on any ranked list, perhaps the gene_set permutation testing mode would provide the increased sensitivity you're looking for. Beyond that I don't think there are any specific algorithmic options that I can suggest.

 

Sorry,

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Alex Lorenzo Starr]

No worries, I figured it was a long shot.  Thanks for taking the time!

Best, Alex.