GOLOCUSID

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John Lande ▴ 280

@john-lande-2357

Last seen 10.2 years ago

dear Bioc, I have retrieved an old stript to extract genes associated with a specific GO term from a previous release of BioC. it exploited the enviroment GOLOCUSID form the package GO. thei enviroment is no longer available in the current release bioc 2.3. is there an equivalent enviroment in some other package? how can I retrieve the genes associated with a specific go term in bioc now. thank you [[alternative HTML version deleted]]

GO GO • 1.4k views

ADD COMMENT • link updated 15.7 years ago by Saroj Mohapatra ▴ 450 • written 15.7 years ago by John Lande ▴ 280

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Saroj Mohapatra ▴ 450

@saroj-mohapatra-1446

Last seen 10.2 years ago

Hi John: I do not have a general answer. However, the "org." packages do have a mapping from GO to Entrez gene. For example, there is the mouse package org.Mm.eg.db that has org.Mm.egGO which maps between the two identifiers. > library("org.Mm.eg.db") > ?org.Mm.egGO2EG ----------- org.Mm.egGO is an R object that provides mappings between entrez gene identifiers and the GO identifiers that they are directly associated with. This mapping and its reverse mapping do NOT associate the child terms from the GO ontology with the gene. Only the directly evidenced terms are represented here. ----------- You could use the appropriate org package for your species. Hope this helps, Saroj ----- Original Message ----- From: "John Lande" <john.lande77@gmail.com> To: bioconductor at stat.math.ethz.ch Sent: Sunday, March 15, 2009 4:29:00 PM GMT -05:00 US/Canada Eastern Subject: [BioC] GOLOCUSID dear Bioc, I have retrieved an old stript to extract genes associated with a specific GO term from a previous release of BioC. it exploited the enviroment GOLOCUSID form the package GO. thei enviroment is no longer available in the current release bioc 2.3. is there an equivalent enviroment in some other package? how can I retrieve the genes associated with a specific go term in bioc now. thank you [[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 -- Computational Biology VBI @ Virginia Tech

ADD COMMENT • link 15.7 years ago Saroj Mohapatra ▴ 450

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Hi John, Saroj is correct in that you should find the mappings you seek in the appropriate organism package ("org.Xx.eg.db" where "Xx" is the initial of the genus and species of the organism you are studying). You probably want to look at the GO2ALLEGS mapping. Marc Saroj K Mohapatra wrote: > Hi John: > > I do not have a general answer. However, the "org." packages do have a mapping from GO to Entrez gene. For example, there is the mouse package org.Mm.eg.db that has org.Mm.egGO which maps between the two identifiers. > >> library("org.Mm.eg.db") >> ?org.Mm.egGO2EG >> > > ----------- > org.Mm.egGO is an R object that provides mappings between entrez > gene identifiers and the GO identifiers that they are directly > associated with. This mapping and its reverse mapping do NOT > associate the child terms from the GO ontology with the gene. > Only the directly evidenced terms are represented here. > ----------- > > You could use the appropriate org package for your species. > > Hope this helps, > > Saroj > > ----- Original Message ----- > From: "John Lande" <john.lande77 at="" gmail.com=""> > To: bioconductor at stat.math.ethz.ch > Sent: Sunday, March 15, 2009 4:29:00 PM GMT -05:00 US/Canada Eastern > Subject: [BioC] GOLOCUSID > > dear Bioc, > > I have retrieved an old stript to extract genes associated with a specific > GO term from a previous release of BioC. > > it exploited the enviroment GOLOCUSID form the package GO. > > thei enviroment is no longer available in the current release bioc 2.3. > is there an equivalent enviroment in some other package? > > how can I retrieve the genes associated with a specific go term in bioc now. > > thank you > > [[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 > >

ADD REPLY • link 15.7 years ago Marc Carlson ★ 7.2k

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thank you very much, for the gene ontology worked. I remeber there was something similar for Kegg pathways. is there something similar now? thank you On Mon, Mar 16, 2009 at 4:52 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > Hi John, > > Saroj is correct in that you should find the mappings you seek in the > appropriate organism package ("org.Xx.eg.db" where "Xx" is the initial > of the genus and species of the organism you are studying). You > probably want to look at the GO2ALLEGS mapping. > > Marc > > > > Saroj K Mohapatra wrote: > > Hi John: > > > > I do not have a general answer. However, the "org." packages do have a > mapping from GO to Entrez gene. For example, there is the mouse package > org.Mm.eg.db that has org.Mm.egGO which maps between the two identifiers. > > > >> library("org.Mm.eg.db") > >> ?org.Mm.egGO2EG > >> > > > > ----------- > > org.Mm.egGO is an R object that provides mappings between entrez > > gene identifiers and the GO identifiers that they are directly > > associated with. This mapping and its reverse mapping do NOT > > associate the child terms from the GO ontology with the gene. > > Only the directly evidenced terms are represented here. > > ----------- > > > > You could use the appropriate org package for your species. > > > > Hope this helps, > > > > Saroj > > > > ----- Original Message ----- > > From: "John Lande" <john.lande77@gmail.com> > > To: bioconductor@stat.math.ethz.ch > > Sent: Sunday, March 15, 2009 4:29:00 PM GMT -05:00 US/Canada Eastern > > Subject: [BioC] GOLOCUSID > > > > dear Bioc, > > > > I have retrieved an old stript to extract genes associated with a > specific > > GO term from a previous release of BioC. > > > > it exploited the enviroment GOLOCUSID form the package GO. > > > > thei enviroment is no longer available in the current release bioc 2.3. > > is there an equivalent enviroment in some other package? > > > > how can I retrieve the genes associated with a specific go term in bioc > now. > > > > thank you > > > > [[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]]

ADD REPLY • link 15.7 years ago John Lande ▴ 280

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Hi John, Because the KEGG pathway IDs have a species specific ID in front of them, those can still be found in KEGG.db. Look for the KEGGPATHID2EXTID and KEGGEXTID2PATHID mappings. Marc John Lande wrote: > thank you very much, > > for the gene ontology worked. I remeber there was something similar > for Kegg pathways. is there something similar now? > > thank you > > > > On Mon, Mar 16, 2009 at 4:52 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> <mailto:mcarlson at="" fhcrc.org="">> wrote: > > Hi John, > > Saroj is correct in that you should find the mappings you seek in the > appropriate organism package ("org.Xx.eg.db" where "Xx" is the initial > of the genus and species of the organism you are studying). You > probably want to look at the GO2ALLEGS mapping. > > Marc > > > > Saroj K Mohapatra wrote: > > Hi John: > > > > I do not have a general answer. However, the "org." packages do > have a mapping from GO to Entrez gene. For example, there is the > mouse package org.Mm.eg.db that has org.Mm.egGO which maps between > the two identifiers. > > > >> library("org.Mm.eg.db") > >> ?org.Mm.egGO2EG > >> > > > > ----------- > > org.Mm.egGO is an R object that provides mappings between > entrez > > gene identifiers and the GO identifiers that they are directly > > associated with. This mapping and its reverse mapping do NOT > > associate the child terms from the GO ontology with the gene. > > Only the directly evidenced terms are represented here. > > ----------- > > > > You could use the appropriate org package for your species. > > > > Hope this helps, > > > > Saroj > > > > ----- Original Message ----- > > From: "John Lande" <john.lande77 at="" gmail.com=""> <mailto:john.lande77 at="" gmail.com="">> > > To: bioconductor at stat.math.ethz.ch > <mailto:bioconductor at="" stat.math.ethz.ch=""> > > Sent: Sunday, March 15, 2009 4:29:00 PM GMT -05:00 US/Canada Eastern > > Subject: [BioC] GOLOCUSID > > > > dear Bioc, > > > > I have retrieved an old stript to extract genes associated with > a specific > > GO term from a previous release of BioC. > > > > it exploited the enviroment GOLOCUSID form the package GO. > > > > thei enviroment is no longer available in the current release > bioc 2.3. > > is there an equivalent enviroment in some other package? > > > > how can I retrieve the genes associated with a specific go term > in bioc now. > > > > thank you > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > <mailto: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 > > > > > >

ADD REPLY • link 15.7 years ago Marc Carlson ★ 7.2k

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