Enrichment of genes in a custom gene set

Question

[ika]

Hello everyone,

I have a gene list of results of a new analysis and would like to test whether these are enriched in the gene lists of previous analyses. This is to serve as a kind of validation of the new method.

I saw the tool WebGestalt allows me to upload my own functional database (which would be my list of previosly identified genes) for gene set enrichment analysis or over-representation analysis.

I'm very unsure how to go about this though. Since I only test for enrichment in one or a handful of gene sets, I'm not sure if this would be appropriate? Also, would gene set enrichment analysis (with a reference set such as the genome) or over-representation analysis be more appropriate?

Any tips are greatly appreciated.

[rpolicastro]

Are the gene lists you are comparing them to gene lists that have some sort of functional annotation associated with them? Or are you just looking at whether there is some sort of significant overlap between the gene sets from different experiments?

[ika]

thank you for your reply, it's the latter - I want to check for a significant overlap.

[rpolicastro]

In that case I would suggest a hypergeometric test.

[ika]

Upon reading more about it, that seems like exactly what I was looking for. Thank you!