[BioC] [biomaRt] contradicting gene information

[Steve Lianoglou]

Hi,

I'm not sure what you're real question is, so I'll try to answer some
potential ones inline:

> I observed the following in a dataset I'm working on:
>
>> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
>> getBM( attributes = c("ensembl_gene_id", "chromosome_name", "strand",
> "start_position", "end_position"), filters = "ensembl_gene_id", values =
> c("ENSG00000002586"), mart = ensembl)
>  ensembl_gene_id chromosome_name strand start_position end_position
> 1 ENSG00000002586               X      1        2609220      2659350
> 2 ENSG00000002586               Y      1        2559220      2609350

That's because:

http://en.wikipedia.org/wiki/Pseudoautosomal_region

> When I check the gene on the ensembl website
> ( http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=1;q=ENSG00000002586 )

When you go to that "search result" page, click through to the gene,
you will also see the Y coord for it as well.

> or web-interface to ensembl biomart ( http://www.ensembl.org/biomart/martview )
>
> I get the coordinates on chromosome X only.
> Any idea as to what might cause this?

Are you asking why biomart is choosing to only show the hit for the X
chromosome and not the Y? I can't venture a guess, but let me venture
a guess:

* Maybe it's just a limitation of web interface?
* Maybe they chose to report X over Y in this view of the query
because everyone has an X, but only 1/2 of the population has a Y?

Or are you asking how it's possible to be on X and Y? The answer to
that is in the wikipedia link above about  the pseudoautosomal regions
...

HTH,

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact