Enrichment analysis and GSEA

Question

[Amr]

In which step is GSEA and enrichment analysis, which should be done before the other and why?

Answer 1

[jared.andrews07]

GSEA stands for gene set enrichment analysis. It's not clear what you mean by "enrichment analysis" here. Regardless, GSEA at minimum needs a ranked set of genes. Certain "enrichment analyses" just need a list of genes. Typically, they're two sides of the same coin and often return similar/complementary results. The order doesn't really matter.

Regardless, we're unlikely to be able to help you without further details.

Answer 2

[MRezaei]

What do you mean by "enrichment analysis"? If you are talking about gene ontology analysis, I think that you should perform a GSEA analysis first. Because, with GSEA analysis, you obtain the significant up and down-regulated genes, and you can achieve the enrichment analysis on mentioned genes.