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.
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?
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.
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.
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.
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?
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.
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.