Pathway enrichment with differential expression p-values

Question

[DVA]

Hello All,

I have a large set of genes with differential expression p-values (from DEseq2) and directional (up or down-regulated) information. I was wondering if anyone knew of a pathway enrichment analysis program that could make use of all of this information rather than just the gene list? Sorry if I have missed an obvious option, but it seems like most of the programs available just use the gene list (like Enrichr) or want to do the entire differential expression calculation from read counts (like GSEA). Does anyone know of a midpoint between these options?

Thank you very much.

Answer 1

[Benn]

There is a nice review in Plos Comp about the different methods that are available for pathway of GO analysis. The methods (with only a list of significant genes) you are referring to are first generation. There are also second and even third generation. Read it in the paper, and you'll know what to look for.

[DVA]

Thanks so much for the information!