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.
What was the original question that triggered the generation of the data/analysis in the first place?
RNA-Seq variant analysis you can perform apart from annotating the DEGs and performing enrichment analysis.
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.
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?
With your list of differentially expressed genes get enriched functions in your experiment using Gene Set Clustering based on Functional annotation (GeneSCF)
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