I have proteome data for a non model organism, and I would like to performe gene onthology (GO) enrichment analysis.
I would like to perform the enrichment for the up-regualted proteins using the all proteins encoded in the genome as background dataset. I downloaded the GO annotation for each protein directly from Uniprot and now I am kind of lost among the many tools available for doing the analysis.
I am looking for web tools or R-Bioconductor tools more appropriate form my purpose, because it seemed to my that most of the tools deal with model organism.
Any advice will be greatly appreciated.