Question: GO enrichement and Ensembl ID
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gravatar for Radhouane Aniba
8.6 years ago by
Radhouane Aniba240 wrote:
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]]
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ADD COMMENTlink modified 8.6 years ago by Maciej Jończyk720 • written 8.6 years ago by Radhouane Aniba240
Answer: GO enrichement and Ensembl ID
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gravatar for Maciej Jończyk
8.6 years ago by
Maciej Jończyk720 wrote:
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
ADD COMMENTlink written 8.6 years ago by Maciej Jończyk720
On 12/05/2011 19:38, mjonczyk at biol.uw.edu.pl wrote: > you can use ontologizer (java application, not in bioconductor). > http://compbio.charite.de/index.php/cmdlineOntologizer.html Or you can use web-based GeneTrail http://genetrail.bioinf.uni-sb.de/ (no need to prepare an association file). It accepts Ensembl IDs out of the box, and does GO, KEGG, miRNA, gene location and couple more, with hypergeometric test that is corrected for multiple testing. One thing it doesn't do is let you specify which branch of GO categories you want to test (it does them all). cheers j -- Jarek Bryk | www.evolbio.mpg.de/~bryk Max Planck Institute for Evolutionary Biology August Thienemann Str. 2 | 24306 Pl?n, Germany tel. +49 4522 763 287 | bryk at evolbio.mpg.de
ADD REPLYlink written 8.6 years ago by Jarek Bryk110
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