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

[James W. MacDonald]

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