Question: An enriched gene in GSEA
0
gravatar for kanwarjag
24 months ago by
kanwarjag950
United States
kanwarjag950 wrote:

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

gsea • 831 views
ADD COMMENTlink modified 24 months ago by h.mon24k • written 24 months ago by kanwarjag950

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?

ADD REPLYlink written 24 months ago by WouterDeCoster38k

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.

ADD REPLYlink written 24 months ago by kanwarjag950

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.

ADD REPLYlink written 24 months ago by WouterDeCoster38k
0
gravatar for h.mon
24 months ago by
h.mon24k
Brazil
h.mon24k wrote:

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.

ADD COMMENTlink modified 24 months ago • written 24 months ago by h.mon24k
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