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 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> -- >>> 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