GSEA analysis for phosphoproteins

Question

[Tarana]

Hi, I did the GSEA analysis . However, none of the pathways follows the FDR cutoff score 0<.25 and p-value. Can I use the data for publication? Such as one of my pathway showing nominal p-value is 0.87 and FDR q-value is 0.89.

Answer 1

[dsull]

Yes, you can use the data and report it. What conclusions you want to draw from it is a separate matter.

[Tarana]

Hi, Thanks for the reply. I run preranked genes list with fold change (comparing treated versus untreated). Actually certain genes are related to the pathway I mentioned above and they are down regulating genes. Based on the FDR and P value can I accept the pathways generated from GSEA for further analysis?

[dsull]

Sure, if you want to explore the pathways further because you find certain genes in the pathway are downregulated, go ahead -- it will be worthwhile to do so.

Your results are not statistically significant, but that doesn't mean it's not biologically significant; sometimes, a single gene with altered gene expression in a pathway is sufficient to alter the entire pathway.