What to do after differential expression

Question

[felipead66]

I often analyse RNA-Seq data and I get to the point of the differentially expressed genes.

My question is whether I can extract more information on these data besides the fold changes.

[Friederike]

What was the original question that triggered the generation of the data/analysis in the first place?

[mks002]

RNA-Seq variant analysis you can perform apart from annotating the DEGs and performing enrichment analysis.

Answer 1

[Charles Warden]

I think Enrichr is a nice, open-source tool for gene enrichment.

It also has an R package, but I would probably start out using the web-version.

You can also test using goseq, but having something with extra modeling for RNA-Seq may not necessarily give you better enrichment results.

If you have a license, IPA is a good option; however, if you don't have a license, I would recommend Enrichr, GATHER, and/or DAVID.

Answer 2

[caggtaagtat]

You could do gene set enrichment analysis (GSEA).

That can give you information whether there is a high abundance of differnetially expressed genes, which belong to a familiar pathway, biological function or cellular structure.

Edit: Or did you generally mean what kind of analysis you can do with RNA-Seq data?

Answer 3

[EagleEye]

With your list of differentially expressed genes get enriched functions in your experiment using Gene Set Clustering based on Functional annotation (GeneSCF)