Say I have done DESeq2 on my RNA-Seq dataset: experimental vs. control
DESeq2 has a column for BH - adjusted Pvalues and I plan to take the genes with less than < 0.05 adj. pvalue and run it with DAVID and use their functional annotation clustering tool.
I run GSEA (ranked by Signal2Noise and permutated by gene type since each condition had only 6 samples each) with the whole gene list against msigdb C5 GO BP gene sets and had the Enrichment Map app ( with permissive parameters such as p-value <0.05 and FDR q-value <0.25 and a overlap coefficient of 0.5) on Cytoscape to visualize the network. I then used AutoAnnotate to annotate clusters based on frequencies of GO BP words in the clusters.
Can I say that the clusters found in DAVID are significant and compare the GO BP terms found in DAVID to GSEA GO BP terms and do analysis?