Recommendations for GSEA leading edge analysis?

Question

[saw44]

I have performed differential expression analysis and gene set enrichment analysis (GSEA) in R using tools such as clusterProfiler.

I would like to perform some further downstream analysis such as Leading Edge analysis, to check for genes overlapping the various enriched gene sets. However, I'm not sure what tools are available.

Does anyone have any recommendations for what I can use for downstream analysis such as leading edge analysis?

Thanks!

Answer 1

[jeffk8900]

Take a look at Enrichment Map. It is a Cytoscape plug-in that visualizes the GSEA results as a network. Instead of looking through tables with individual gene sets, this app converts that to an overlapping network of gene sets. Allows the viewing of sets that have gene overlaps (leading edge), and provides a more useful output for interpretation. baderlab.org/Software/EnrichmentMap

Cheers.