[BioC] Simple pathway enrichment analysis for gene lists

[Enrico Ferrero]

Dear list,

Can anybody suggest how to perform a simple pathway enrichment
analysis starting from a list of gene IDs?

I know about the gage and ROntoTools packages that use KEGGREST to
retrieve an up to date version of the KEGG database, but, as far as I
understand, they require a microarray experiment as input (or at least
fold changes and pvalues).

Since this time around I'm not starting from a microarray experiment
but I just have a gene list, I'm looking for a way to perform pathway
enrichment analysis using a simple numerical method such as Fisher's /
hypergeometric test.

I know the Category package still provides a KEGGHyperG class (which
would be perfect!), but the results are based on the outdated version
of KEGG (via KEGG.db, I guess).

Are there any good alternatives available out there? Would it be
possible to use reactome.db in conjunction with the Category/GOstats
functions for example?

Thank you!
Best,

-- 
Enrico Ferrero
Department of Genetics
Cambridge Systems Biology Centre
University of Cambridge