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 -- [[alternative HTML version deleted]]

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