[BioC] chrome coordinates are not same between Ensembl and Affy's annotation file

[James W. MacDonald]

Hi Shirley,

shirley zhang wrote:
> Hi James,
> 
> Thank you vey much for your quick reply.
> 
> Yes. You are right, Affy's annotation is based on NCBI build 36. Do
> you know which version of Ensembl is close to Affy's annotation? Since
> I have the coordinates for many probes from Affy's exon array, it
> would be much easier for me to map Affy's probe location to
> Ensemble's.

How about Ensembl 51?

 > mart <- useMart("ensembl_mart_51", dataset="hsapiens_gene_ensembl",
host="may2009.archive.ensembl.org",path="/biomart/martservice", 
archive=TRUE)
Checking attributes ... ok
Checking filters ... ok
 > getBM(c("ensembl_gene_id", "external_gene_id", "start_position", 
"end_position"), "hgnc_symbol", "SFRS1", mart)
   ensembl_gene_id external_gene_id start_position end_position
1 ENSG00000136450            SFRS1       53433283     53439706

Best,

Jim


> 
> Thanks again,
> Shirley
> 
> 
> On Thu, Sep 24, 2009 at 2:52 PM, James W. MacDonald
> <jmacdon at med.umich.edu> wrote:
>> Hi Shirley,
>>
>> shirley zhang wrote:
>>> Dear List,
>>>
>>> I have been trying to draw the genome graphs for some genes in human.
>>> I found that the coordinates of some genes are not close between
>>> Ensembl and Affy's annotation (Affymetrix Human Exon array). For
>>> example, gene SFRS1:
>>>
>>> SFRS1 (ENSG00000136450):     Chromosome 17: 56,078,284-56,084,707
>>> reverse strand  (Ensemble 55)
>>>
>>> SFRS1Transcript Cluster ID: 3764103  Human Exon 1.0 ST):
>>> chr17:53421412-53439635 (-)
>>>
>>> Can anybody tell me what happens?
>> Sure. Things change. If you query the UCSC genome browser using NCBI build
>> 36, you get
>>
>> SFRS1 (uc002ivj.1) at chr17:53433279-53439706 - splicing factor,
>> arginine/serine-rich 1 isoform
>> SFRS1 (uc002ivi.1) at chr17:53433279-53439706 - splicing factor,
>> arginine/serine-rich 1 isoform
>>
>>
>> If you then try the newer build (GRCh37) you get
>>
>> SFRS1 at chr17:56078282-56084707 - (NM_006924) splicing factor,
>> arginine/serine-rich 1 isoform
>> SFRS1 at chr17:56078282-56084707 - (NM_001078166) splicing factor,
>> arginine/serine-rich 1 isoform
>>
>> The affy annotation is based on older information than Ensembl.
>>
>>
>> Best,
>>
>> Jim
>>
>>
>>> Thanks,
>>> Shirley
>>>
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>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>>
> 
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826