I performed a GO enrichment analysis (Fisher’s Exact Test; FDR<0.05; Pvalue<0.001) in B2G using as test set the up-regulated differentially expressed genes (DEGs) in each comparison of each treatment meanwhile the whole set of DEGs of the experiment were considered as reference set.
I believe that if I would like to know the significant functional characteristics of the DEGs of each comparison, as I did should be OK. But, should I have performed the enrichment analysis to the overall transcriptome (as reference set) in order to increase the power of the test ??
Any advise would be highly appreciate!!
Thanks so much