[BioC] GO enrichement and Ensembl ID

[mjonczyk at biol.uw.edu.pl]

Hi Radhouane,

you can use ontologizer (java application, not in bioconductor).
http://compbio.charite.de/index.php/cmdlineOntologizer.html

You just have to prepare association file (linking EnsemblIDs to GO-terms) as
described at GO site:
http://www.geneontology.org/GO.format.gaf-1_0.shtml

Program performs hypergeometric test, correction on tree hierarchy and multiple
comparisons can be used. Program produces also graphs.

Hope it helps,

>Hi everyone,
>
>I am browsing a lot of BioC packages for GO and KEGG enrichmet, (GOstats etc
>..), and almost all of them consider gene lists in EntrezID format, I have
>EnsemblID gene list, and I am facing the problem of 1 to Many conversion
>(Same EnsemblID could have many EntreIDs (transcripts) )
>
>Is there any enrichment tool or package in BioC that consider gene lists in
>EnsemblID formats ?
>
>Thank you
>
>Radhouane