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

[shirley zhang]

Hi Jim,

It works. Thanks a lot. Shirley

On Thu, Sep 24, 2009 at 4:25 PM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> 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
>



-- 
Xiaoling (Shirley) Zhang

Ph.D. Candidate in Bioinformatics
Boston University, Boston, MA
Tel: (857) 233-9862	
Email: zhangxl at bu.edu