[BioC] How do you find your orthologues?

[Hans-Rudolf Hotz]

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
>
>