Entering edit mode
4.5 years ago
O'kin-1
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20
I am just wondering if it's acceptable to conduct enrichment analysis for just one interesting gene out of a list of about one hundred genes. I know this is do-able but I just want to know if it's acceptable to do that.
Thanks.
What do you mean by conducting enrichment analysis for just one gene? I've always understood that enrichment analysis are meant to assess the enrichment of a subset of several genes in a wider list of genes.
User may simply mean to look up the pathways, gene ontologies, et cetera to which their gene of interest belongs, but one can not obviously obtain any p-value for this. O'Kin-1, I would simply conduct a literature search for your gene of interest - have the days of literature searches vanished...? These were a lot easier when we were not generating results so rapidly, with hundreds or thousands of genes. If you want, you could also simply go to the GO, KEGG, et cetera web-sites and search for your single gene there.
Kevin Blighe, thanks a lot for your response. You actually understood the point I was making. Even though I have not gathered the confidence to publish such an approach in the literature, I have found it so much more efficient and fast than literature time and time again. In my latest use of this approach, the "single gene" enrichment analysis (pardon my contraption) actually revealed other valid interesting functions of that one particular gene which would have taken me one week of deeply scouring the literature to find.
In a nutshell, while the functions of my one gene of interest have been documented in the literature and would have taken me roughly one week of deep literature search to find, conducting enrichment analysis for it led me to these functions in just roughly 1 hour.
Yes, I agree that it can quicken the process. You can still use this technique and not necessarily report it. It is essentially just an aid to help understand the data. The assumption would be, however, that your conclusion will not be solely formed on, for example, a single gene-to-GO term assignment.