An enriched gene in GSEA

Question

[kanwarjag]

I performed a GSEA analysis on set of differentially expressed genes and one of the gene in a pathway is not present in literature/ gene sets. Is it possible? How can we explain this.

Thanks

[WouterDeCoster]

I'm not sure how to interpret your question. Is one of your differential expressed genes not in a gene set? Or did you find a gene in a gene set which you can't explain?

[kanwarjag]

There is a gene X we found to be associated with a particular pathway after GSEA. However a search of literature and GSEA datasets do not have the said gene. But that gene is present in our differentially expressed genes.

[WouterDeCoster]

Well, there probably was a (good) reason to include "gene X" in that "particular pathway". I can't help further since I have no idea about which gene, which pathway, which geneset. The genesets probably contain some information on how these were made.

Answer 1

[h.mon]

By the very definition of GSEA, it is impossible, as the gene sets are defined a priori:

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

The gene would not be in the pathway if it weren't present in literature/ gene sets.