Pathway enrichment analysis for a small set of genes

Question

[Raheleh]

Hello all,

I have a gene signature (49 genes) which can stratify my patients in Relapse and non-Relapse cases. I got this signature using PAMR method. Now I want to know these 49 gene are related to which biological pathway. Except DAVID and Reactome, what else I can use? Can I use GSEAPrerank tool?

Any help or suggestion will be very appreciated!

Answer 1

[dsull]

In GSEA (or GSEAPrerank), you have to supply an entire ranked gene list; you have to use ALL your genes not just 49 genes. For 49 genes, something like Gene Ontology overrepresentation analysis would be more appropriate.

My favorite tool for such analysis is EnrichR:

https://amp.pharm.mssm.edu/Enrichr/

It's up-to-date, well-maintained, and gives you comprehensive enrichment results (it will perform enrichment across a variety of databases: GO, KEGG, Wikipathways, and much much more).