[BioC] Help in BioMart

[steffen at stat.Berkeley.EDU]

Dear David,

The ensembl helpdesk at helpdesk at ensembl.org is probably the best place 
to answer your question.  There are genes that have overlapping exons,
sometimes these are on the same strand, sometimes they are on opposite
strands so it is possible for a SNP to fall in two genes.  The genes you
mention seem to be very close to each other and thus possible share some
common genomic sequence. You could investigate this starting here:

http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000078808

Hope this helps.

Steffen
> Dear Steffen,
> I am sorry to bother you as I guess you should recieve many emails.
> I am using your biomart code and I am facing a little problem when using
> the
> getBM function to recover information about one SNP. In particular, given
> a
> rsnumber, I am interested in finding the gene it belongs to. However,
> frequently, not a single gene is given.
> For example, with the rs7515488
> tmp  <- getBM(attributes =
> c("refsnp_id","chr_name","snp_allele","ensembl_external_gene_id","chrom_star
> t"),
>               filters = "refsnp",
>               values = c("rs7515488"),
>               mart = mart)
>
> Provides me with two output lines, one corresponding to the SDF4 and the
> other the B3GALT6 genes.
> Do you known how I can solve this issue so that the SNP belongs to only
> one
> gene, the one corresponding to dbSNP for example which should be SDF4 .
>
> Your help will be deeply appreciated.
> Best
> David
>
> Tregouet David
> INSERM U525
> Faculté de Médecine Pitié-Salpêtrière,
> 91 Boulevard de l’Hopital
> 75634 Paris Cedex 13
> France
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>
>