2011/5/5 Steve Lianoglou <mailinglist.honeypot@gmail.com>

> Hi,
>
> On Thu, May 5, 2011 at 12:25 PM, Radhouane Aniba <aradwen@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.
>


What is the universe of gene ids ? what does is it means ?


>
> 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
>



-- 
*Radhouane Aniba*
*Bioinformatics Postdoctoral Research Scientist*
*Institute for Advanced Computer Studies
Center for Bioinformatics and Computational Biology* *(CBCB)*
*University of Maryland, College Park
MD 20742*

	[[alternative HTML version deleted]]

