I'm interested in comparing the genes and genes sets regulated by two different drugs. I performed a microarray on Drug A vs control, and Drug B vs control. Using Limma, I calculated the differential expression for all 20,000 genes, and performed a pre-ranked GSEA. I now have ~700 gene sets that are depleted by Drug A, and ~800 gene sets that are depleted by Drug B (FDR<0.05). There are ~280 gene sets that are depleted by both Drug A and Drug B.
Taking the pre-ranked GSEA output, how can I meaningfully compare these 280 gene sets depleted by both treatments to characterize similarities and differences between these treatments.
If I am interested in PI3K signaling, could I compare the Normalized Enrichment Scores (NES) for all of the gene sets involved in PI3K signaling and perform a Wilcoxon test to determine if there is different enrichment between the two treatments?
Can I take the number of genes within a gene set regulated by each drug and meaningfully compare those gene sets?
Thank you for the help, a few pointers or a publication will set me on the right track. I've searched and can't find analyses like this.