Hello,

we performed WES on different samples, which results in a different gene lists which show which genes are mutated in the respective biopsy.

I would like to compare two samples to one another and check, if for example a certain pathway/GO term carries more mutation than one might expect by chance. For this, I wanted to perform a GSEA. However, I am very new to this, and I wasn't quite sure what to do exactly. One Challenge is, that my gene list is unranked, and it feels like the majority of tools prefer a ranked gene list as an input. Another question I have, is what the appropriate "background" for this type of analysis (mutated genes in sample 1 vs mutated genes in sample 2) would be and how to perform this analysis in general.

Lastly, are there any other kinds of analysis I could do with these gene lists?

Any help is much appreciated!

Best