Question: An enriched gene in GSEA
0
gravatar for kanwarjag
2.5 years ago by
kanwarjag1000
United States
kanwarjag1000 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 • 971 views
ADD COMMENTlink modified 2.5 years ago by h.mon27k • written 2.5 years ago by kanwarjag1000

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 2.5 years ago by WouterDeCoster41k

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 2.5 years ago by kanwarjag1000

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 2.5 years ago by WouterDeCoster41k
0
gravatar for h.mon
2.5 years ago by
h.mon27k
Brazil
h.mon27k 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 2.5 years ago • written 2.5 years ago by h.mon27k
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