Hello,

I've come across several gene set enrichment tools aimed at summarizing DE genes in RNA-seq datasets, but I have a slightly different goal, and I'm wondering if any of the available tools are suitable.

I have several non-model organisms for which I've generated KEGG KO identifiers for. Instead of looking for significant differences in expression within a genome, I'm hoping to summarize significant differences between species based on KO presence/absence. For instance, one lineage has many more genes associated with flagellar function, whereas another has a more complete photosynthetic apparatus.

Maybe this question doesn't make any sense at all, but any input would be appreciated.

Thanks!

Ryan

If I understood you correctly you want to compare if your organism has more genes or less in the same KO terms.

You could use BioCor package using mpathSim to compare if between the same KO terms despite having different genes are still similar between them. It is not the same as you requested, but perhaps is close enough to see the differences between species. (Disclaimer, I am the author of BioCor) I am developing a new package here that aims to compare GeneSetCollections (that would be one collection for each specie you have), and I will try to develop there a method for this case.