Gene enrichment analysis for metagenome (non-model organisms)

Question

[TomM]

Hi all

Is there a way to run a gene enrichment analysis on a non model organism metagenome? I have functional annotations (GO and KO) and looked into Panther and GOrilla, but it seems they only work with reference gene lists of selected model organisms. This won't work, as I have many different non model organisms in my metagenome. Are there tools or packages that allow uploading my own reference list of GO or KO ids and then running enrichment analyses based on that?

Thanks!

Answer 1

[andres.firrincieli]

Hi Tom,

for GO enrichment analysis you could use topGO

[TomM]

Thanks, I will give it a try!