I am sorry if this question is a duplicate - I could not find anything that match exactly this,
I am trying to find genomic differences between two conditions (response to therapy). And I was not able to find a difference on gene level (cohort size is not that big, each gene is affected only in couple of samples out of hundred and thus the data is sparse). Then I am trying to somehow meaningfully join different genes so the dataset becomes less "sparse".
I was thinking that probably a specific pathway was damaged in non-responders, but the tools I am checking now are taking a list of enriched genes as input and then do pathway enrichment analysis - while, as I said, I found nothing significant at gene level.
Question: Can I annotate my list of genes with different pathway information (to which pathway this gene belongs) and perform pathway enrichment analysis from that point (e.g. the same pathway was damaged 50% of times in one group and 10% in other - it would be a result!)? Which tool can be used for this?