I am performing the GO/pathway analysis of my RNA-seq data using GSEA. I have many DEGs, about 3000 in total, and I got many enriched pathways with both positive and negative NES. However, all or most of the enriched pathways have an FDR > 0.05 and therefore are not classified as statistically significant. Most of such enriched pathways are characterized by more than 30 DEGs, which is a reasonable number of differentially expressed genes associated with a certain pathway.
What could be the reason for that?
I would gladly appreciate any comment or suggestion and thanks in advance!