I clustered proteins (and their corresponding genes) from an Matrix with Protein expression changes in different experimental settings from E.Coli. Proteins, that correspond in their expression changes should be together in a cluster.

I want to evaluate the clusters/gen lists using a functional enrichment analysis / GO analysis / Pathway analysis / KEGG and so on.... So I enter my gen list, all genes detected in the experiment and a GO-Term list or another functional list. The result would be a score, which category is enriched in the set. (Which would give a hint about the cluster quality)

DAVID has all the function I need, but I read, that it is no longer up to date. Also I want to check many sets in an automated way. And I want to be able to plot my results. So I think an Python or R implementation would be better (I prefer Python). Is there maybe a module, that can do the same analysis as DAVID?