Hi everybody,

I have proteome data for a non model organism, and I would like to perform 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.
An update.

I used the Bioconductor package [topGO][1] and I think it is a great tool for performing enrichment for non model organisms.

 [1]: http://www.bioconductor.org/packages/release/bioc/html/topGO.html