[BioC] Gene Lists and Genomes

[Steve Lianoglou]

Hi,

On Thu, May 5, 2011 at 12:25 PM, Radhouane Aniba <aradwen at gmail.com> wrote:
> Thanks Tim,
>
> Actually I have a predicted list of miRNA binding sites targetting specific
> genes in 4 genomes.
>
> What I am trying to find is the characteristics of these Genes {g} for a
> specific genome {G} in term of GO enrichement and KEGG enrichment.
>
> My starting point is a file with a list of ENSEMBL IDs, just that, no
> annotation and no scores, just the gene names.
>
> I am looking for the right package to do that, topGO for example seems to
> not accept only gene names, annotation is needed as well as other details, I
> am acually reading about all these packages that make gene enrichment
> analyses.

It seems as if you can use GOstats for this purpose, but you'd first
need to convert these IDs to entrez id (which you can do using the
appropriate org.*.eg.db pacakge (org.Hs.eg.db if we're talking about
human, for example).

In addition to this 'target list' you have, you'll need a appropriate
way to define "the universe" of gene id's to use for testing.

Given those two lists (targets and universe) you'll be able to run
GOstats to get GO enrichment for your targets. Incidentally, you
should also be able to use GOstats for KEGG ... see the vignettes
here:

http://www.bioconductor.org/packages/release/bioc/html/GOstats.html

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact