Comparing the whole genelist by GSEA GO BP terms to adjusted pvalue genelist by DAVID GO BP terms

Question

[minifoog]

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?

Answer 1

[xanderpico]

Since you tagged 'cytoscape', I'll share a common Cytoscape approach to this type of analysis that just uses STRING and related enrichment services:

1. Paste your DE genes into the STRING protein search tool in Cytoscape (via stringApp)
2. Load your data onto the network
3. Update data visualization styles per your taste
4. Perform functional enrichemnt analysis using the same stringApp

Now you have enrichment analysis results across multiple up-to-date resources and you can run EnrichmentMap with a click from the stringApp results table as well.

See exercise 1 in this tutorial for more details: https://cytoscape.org/cytoscape-tutorials/protocols/differentially-expressed-genes/#/ex1-up-string

[minifoog]

Thanks for the comment, I’ll look into this method