How to make my own GO.db?
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Xiaohui Wu ▴ 280
@xiaohui-wu-4141
Last seen 6.6 years ago
Hi all, There are some GO databases 'org.Hs.eg.db' available in Biocondutor, which can be used in some R packages like goProfiles. But I need to analyse the GO terms in Chlamy, and no corresponding GO db can be found. Is there any document describing how to make GO db, I googled, but none was found. Or, is there any other way like using perl to relate the GO terms and genes and do some hypothesis tests between two groups of genes? Thanking you, Rae [[alternative HTML version deleted]]
GO goProfiles GO goProfiles • 572 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 4.7 years ago
United States
Hi Rae, Are you looking for the GO.db package? http://www.bioconductor.org/packages/release/data/annotation/html/GO.d b.html Marc On 06/25/2010 02:06 PM, Xiaohui Wu wrote: > Hi all, > > There are some GO databases 'org.Hs.eg.db' available in Biocondutor, which can be used in some R packages like goProfiles. But I need to analyse the GO terms in Chlamy, and no corresponding GO db can be found. > > Is there any document describing how to make GO db, I googled, but none was found. Or, is there any other way like using perl to relate the GO terms and genes and do some hypothesis tests between two groups of genes? > > Thanking you, > > Rae > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 4.7 years ago
United States
Hi Rae, It occurs to me that you might be referring to//// <http: www.chlamy.org=""/> Chlamydomonas, in which case you will be using an unsupported organism. We have some support for those however if you look at the vignette in the file "GOstatsForUnsupportedOrganisms.pdf" in the GOstats package: http://www.bioconductor.org/packages/release/bioc/html/GOstats.html You will have to find or generate a mapping between the genes for your organism and the GO terms though. You might want to check the blast2GO project for that. Marc On 06/25/2010 02:06 PM, Xiaohui Wu wrote: > Hi all, > > There are some GO databases 'org.Hs.eg.db' available in Biocondutor, which can be used in some R packages like goProfiles. But I need to analyse the GO terms in Chlamy, and no corresponding GO db can be found. > > Is there any document describing how to make GO db, I googled, but none was found. Or, is there any other way like using perl to relate the GO terms and genes and do some hypothesis tests between two groups of genes? > > Thanking you, > > Rae > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
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