Hi Marc,

Thank you for the response. Sorry for the confusion, but what I actually
wanted to do was perform enrichment analysis using uniprot accessions
instead of entrez id's. There's another package, topGO, which allows one to
specify a universe of id's, the mapping between id's and their GO terms and
a list of interesting genes (with their associated uniprot id's).

I believe that package also uses GOdb to resolve the topology for each
ontology. However, I would like to use the hypergeometric test instead of
their available suite of tests.

Hope that clears things up!

Thanks,
Paul

On Thu, Feb 10, 2011 at 11:00 AM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Paul,
>
> We don't presently have that capability built into our Category testing
> functionality.  We can test, GO, KEGG and I believe even PFAM, but there
> is nothing presently there for Uniprot.  But I must also admit that your
> request surprised me a bit because Uniprots are accessions and do not
> (as I understand them) represent "families" or "categories" that genes
> could be grouped into.  So I am a little bit perplexed about how they
> would be used to represent categories of genes?  Is there possibly some
> other information inside of a more complete uniprot record that can be
> used in this way and which I am overlooking?  If so, then that
> represents another challenge that will have to be overcome in order for
> what you ask to become possible.
>
>
>  Marc
>
>
>
> On 02/08/2011 04:24 PM, Paul Rigor wrote:
> > Hello,
> >
> > How would I configure a hypergeom object to use uniprot ids for both the
> > universe of genes and the list of interesting genes?
> >
> > Thanks!
> > Paul
> >
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