Gene symbol converter/translator
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Anh Tran ▴ 90
@anh-tran-2795
Last seen 9.7 years ago
Hi all, I'm wondering if there is any package that translate the gene symbol into its full name. The result would look something like this page (for the gene name) http://www.genecards.org/cgi-bin/previous/carddisp.pl?gene=OLIG2 Thanks -- Regards, Anh Tran [[alternative HTML version deleted]]
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 7.8 years ago
United States
Hi Anh, Bioconductor provides many packages to let you do that. To find out more about these packages you might want to look here: http://www.bioconductor.org/packages/2.2/bioc/html/AnnotationDbi.html And here you can find the latest release of these annotations packages: http://www.bioconductor.org/packages/2.2/data/annotation/ If you are looking to translate human mappings, as in your web page then you might want to try this package: http://www.bioconductor.org/packages/2.2/data/annotation/html/org.Hs.e g.db.html And finally, if you use that specific package you will probably want to pay attention to the org.Hs.egGENENAME, org.Hs.egSYMBOL, and org.Hs.egALIAS2EG mappings. to get information about your question. Other annotation packages will have similar mappings available. Marc Anh Tran wrote: > Hi all, > > I'm wondering if there is any package that translate the gene symbol into > its full name. > The result would look something like this page (for the gene name) > http://www.genecards.org/cgi-bin/previous/carddisp.pl?gene=OLIG2 > > Thanks > >
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Thanks. That was helpful. Save me from downloading HUGO database and loading them into MySQL. Best, Anh On Mon, Jul 7, 2008 at 3:41 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > Hi Anh, > > > Bioconductor provides many packages to let you do that. To find out more > about these packages you might want to look here: > > http://www.bioconductor.org/packages/2.2/bioc/html/AnnotationDbi.html > > > And here you can find the latest release of these annotations packages: > > http://www.bioconductor.org/packages/2.2/data/annotation/ > > > If you are looking to translate human mappings, as in your web page then > you might want to try this package: > > > http://www.bioconductor.org/packages/2.2/data/annotation/html/org.Hs .eg.db.html > > > And finally, if you use that specific package you will probably want to pay > attention to the org.Hs.egGENENAME, org.Hs.egSYMBOL, and org.Hs.egALIAS2EG > mappings. to get information about your question. Other annotation packages > will have similar mappings available. > > > Marc > > > > > Anh Tran wrote: > >> Hi all, >> >> I'm wondering if there is any package that translate the gene symbol into >> its full name. >> The result would look something like this page (for the gene name) >> http://www.genecards.org/cgi-bin/previous/carddisp.pl?gene=OLIG2 >> >> Thanks >> >> >> > > -- Regards, Anh Tran [[alternative HTML version deleted]]
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