How do you find your orthologues?
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k. brand ▴ 420
@k-brand-1874
Last seen 9.9 years ago
Esteemed Bioconductor UseRs and Devs, How do you find your orthologues? We have a variety of data (proteomic, expression) from a variety of species (mouse, rat, pig, human) with lots of primary identifiers (GI-number, ensembl gene ID, gene-symbol). What we need to do is take such an identifier, say a mouse ensembl gene ID, and have a list of identifers for the mapped orthologue (to say rat and pig) returned. It seems compara will do this, via a Perl API http://www.ensembl.org/info/docs/api/compara/index.html Can it also be accessed via R/BioConductor? WHich package? BiomaRt? Or is there another BioConductor package employed for this task i should be looking at? With thanks in advance for tips and reflections before i spend another day hunting for a package to achieve this, Karl -- Karl Brand Dept of Cardiology and Dept of Bioinformatics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam T +31 (0)10 703 2460 |M +31 (0)642 777 268 |F +31 (0)10 704 4161
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@hotz-hans-rudolf-3951
Last seen 3.8 years ago
Switzerland
Hi Karl Yes, you can do it with biomaRt. Have a look at the 'getLDS' function. quick example: > library(biomaRt) > > ensembl <- useMart("ensembl") > > human = useDataset("hsapiens_gene_ensembl", mart=ensembl) > mouse = useMart("ensembl", dataset="mmusculus_gene_ensembl") > > getLDS(attributes=c("ensembl_gene_id"), filters="ensembl_gene_id", values=c("ENSMUSG00000021111"), mart=mouse,attributesL=c("hgnc_symbol", "ensembl_gene_id"), martL=human) V1 V2 V3 1 ENSMUSG00000021111 PAPOLA ENSG00000090060 > Hope this helps Regards, Hans On 06/26/2012 12:43 PM, Karl Brand wrote: > Esteemed Bioconductor UseRs and Devs, > > How do you find your orthologues? > > We have a variety of data (proteomic, expression) from a variety of > species (mouse, rat, pig, human) with lots of primary identifiers > (GI-number, ensembl gene ID, gene-symbol). What we need to do is take > such an identifier, say a mouse ensembl gene ID, and have a list of > identifers for the mapped orthologue (to say rat and pig) returned. It > seems compara will do this, via a Perl API > > http://www.ensembl.org/info/docs/api/compara/index.html > > Can it also be accessed via R/BioConductor? WHich package? BiomaRt? Or > is there another BioConductor package employed for this task i should be > looking at? > > With thanks in advance for tips and reflections before i spend another > day hunting for a package to achieve this, > > Karl > >
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@alessandro-brozzi-5276
Last seen 9.5 years ago
European Union
hi Karl, another possible solution might be the package "HomoVert": http://labs.fhcrc.org/fero/R/HomoVert.html that contains a Homologene (NCBI ) conversion table (currently Build 64) and functions that use this table to convert Entrez Gene IDs from one species to another. Alex On Tue, Jun 26, 2012 at 12:43 PM, Karl Brand <k.brand@erasmusmc.nl> wrote: > Esteemed Bioconductor UseRs and Devs, > > How do you find your orthologues? > > We have a variety of data (proteomic, expression) from a variety of > species (mouse, rat, pig, human) with lots of primary identifiers > (GI-number, ensembl gene ID, gene-symbol). What we need to do is take such > an identifier, say a mouse ensembl gene ID, and have a list of identifers > for the mapped orthologue (to say rat and pig) returned. It seems compara > will do this, via a Perl API > > http://www.ensembl.org/info/**docs/api/compara/index.html<http: www="" .ensembl.org="" info="" docs="" api="" compara="" index.html=""> > > Can it also be accessed via R/BioConductor? WHich package? BiomaRt? Or is > there another BioConductor package employed for this task i should be > looking at? > > With thanks in advance for tips and reflections before i spend another day > hunting for a package to achieve this, > > Karl > > > -- > Karl Brand > Dept of Cardiology and Dept of Bioinformatics > Erasmus MC > Dr Molewaterplein 50 > 3015 GE Rotterdam > T +31 (0)10 703 2460 |M +31 (0)642 777 268 |F +31 (0)10 704 4161 > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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k. brand ▴ 420
@k-brand-1874
Last seen 9.9 years ago
Bruce, Hans, Alex, Many thanks for the tips and the example. Both biomaRt and HomoVert look excellent to map across species. But, and i could be wrong, i could be out of luck for for a direct mapping to/from GI numbers. I'll either be back with a solution. Or a new thread :) Thanks again, Karl On 26/06/12 12:47, Bruce Moran(External) wrote: > Hi Karl, > > biomaRt is great for this: > > http://www.bioconductor.org/packages/2.2/bioc/vignettes/biomaRt/inst /doc > /biomaRt.pdf > > Pretty nice walkthroughs in the manual above too. > > Good luck, > > Bruce. > > -----Original Message----- > From: bioconductor-bounces at r-project.org > [mailto:bioconductor-bounces at r-project.org] On Behalf Of Karl Brand > Sent: 26 June 2012 11:43 > To: bioconductor at r-project.org > Subject: [BioC] How do you find your orthologues? > > Esteemed Bioconductor UseRs and Devs, > > How do you find your orthologues? > > We have a variety of data (proteomic, expression) from a variety of > species (mouse, rat, pig, human) with lots of primary identifiers > (GI-number, ensembl gene ID, gene-symbol). What we need to do is take > such an identifier, say a mouse ensembl gene ID, and have a list of > identifers for the mapped orthologue (to say rat and pig) returned. It > seems compara will do this, via a Perl API > > http://www.ensembl.org/info/docs/api/compara/index.html > > Can it also be accessed via R/BioConductor? WHich package? BiomaRt? Or > is there another BioConductor package employed for this task i should be > > looking at? > > With thanks in advance for tips and reflections before i spend another > day hunting for a package to achieve this, > > Karl > > -- Karl Brand Dept of Cardiology and Dept of Bioinformatics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam T +31 (0)10 703 2460 |M +31 (0)642 777 268 |F +31 (0)10 704 4161
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Hi Karl, You might also look at the hom.Xx.inp.db packages, which map orthologues via InParanoid. There is a convenience function inpIDMapper() in AnnotationDbi that does the mappings. Or you could have some SQL fun and do your own ;-D Best, Jim On 6/26/2012 12:20 PM, Karl Brand wrote: > Bruce, Hans, Alex, > > Many thanks for the tips and the example. > > Both biomaRt and HomoVert look excellent to map across species. But, > and i could be wrong, i could be out of luck for for a direct mapping > to/from GI numbers. > > I'll either be back with a solution. Or a new thread :) > > Thanks again, > > Karl > > > On 26/06/12 12:47, Bruce Moran(External) wrote: >> Hi Karl, >> >> biomaRt is great for this: >> >> http://www.bioconductor.org/packages/2.2/bioc/vignettes/biomaRt/ins t/doc >> /biomaRt.pdf >> >> Pretty nice walkthroughs in the manual above too. >> >> Good luck, >> >> Bruce. >> >> -----Original Message----- >> From: bioconductor-bounces at r-project.org >> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Karl Brand >> Sent: 26 June 2012 11:43 >> To: bioconductor at r-project.org >> Subject: [BioC] How do you find your orthologues? >> >> Esteemed Bioconductor UseRs and Devs, >> >> How do you find your orthologues? >> >> We have a variety of data (proteomic, expression) from a variety of >> species (mouse, rat, pig, human) with lots of primary identifiers >> (GI-number, ensembl gene ID, gene-symbol). What we need to do is take >> such an identifier, say a mouse ensembl gene ID, and have a list of >> identifers for the mapped orthologue (to say rat and pig) returned. It >> seems compara will do this, via a Perl API >> >> http://www.ensembl.org/info/docs/api/compara/index.html >> >> Can it also be accessed via R/BioConductor? WHich package? BiomaRt? Or >> is there another BioConductor package employed for this task i should be >> >> looking at? >> >> With thanks in advance for tips and reflections before i spend another >> day hunting for a package to achieve this, >> >> Karl >> >> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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