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Question: symbol to location
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gravatar for Rafael A. Irizarry
10.9 years ago by
Rafael A. Irizarry2.3k wrote:
Hi! Can you recommend your favorite way to go from gene symbols, such as AATK, ABCB1, etc.. to genomic location? what ive come up with seems way to cumbersome. -r
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ADD COMMENTlink modified 10.9 years ago by Steffen Durinck580 • written 10.9 years ago by Rafael A. Irizarry2.3k
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gravatar for Steffen Durinck
10.9 years ago by
Steffen Durinck580 wrote:
Hi Rafa, You can do this easily with biomaRt, here's the code: library(biomaRt) ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl") symbols = c("AATK","ABCB1") getBM(c("hgnc_symbol","chromosome_name","start_position","end_position ","band","strand"), filters="hgnc_symbol", values=symbols,mart=ensembl) it gives: > hgnc_symbol chromosome_name start_position end_position band strand 1 AATK 17 76705703 76754467 q25.3 -1 2 AATK 17 76705703 76754467 q25.3 -1 3 ABCB1 7 86970884 87180500 q21.12 -1 Note that AATK is twice in the output because it has 2 transcripts in Ensembl. best, Steffen Rafael A Irizarry wrote: > Hi! > > Can you recommend your favorite way to go from > gene symbols, such as AATK, ABCB1, > etc.. to genomic location? > > what ive come up with seems way to cumbersome. > > -r > > _______________________________________________ > 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 > -- Steffen Durinck, Ph.D. Oncogenomics Section Pediatric Oncology Branch National Cancer Institute, National Institutes of Health URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ Phone: 301-402-8103 Address: Advanced Technology Center, 8717 Grovemont Circle Gaithersburg, MD 20877
ADD COMMENTlink written 10.9 years ago by Steffen Durinck580
perfect. thanks -r On Tue, 26 Dec 2006, Steffen Durinck wrote: > Hi Rafa, > > You can do this easily with biomaRt, here's the code: > > library(biomaRt) > ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl") > symbols = c("AATK","ABCB1") > getBM(c("hgnc_symbol","chromosome_name","start_position","end_positi on","band","strand"), > filters="hgnc_symbol", values=symbols,mart=ensembl) > > it gives: > >> hgnc_symbol chromosome_name start_position end_position band strand > 1 AATK 17 76705703 76754467 q25.3 -1 > 2 AATK 17 76705703 76754467 q25.3 -1 > 3 ABCB1 7 86970884 87180500 q21.12 -1 > > Note that AATK is twice in the output because it has 2 transcripts in > Ensembl. > > best, > Steffen > > Rafael A Irizarry wrote: >> Hi! >> >> Can you recommend your favorite way to go from gene symbols, such as AATK, >> ABCB1, etc.. to genomic location? >> >> what ive come up with seems way to cumbersome. >> >> -r >> >> _______________________________________________ >> 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 >> > > > -- > Steffen Durinck, Ph.D. > > Oncogenomics Section > Pediatric Oncology Branch > National Cancer Institute, National Institutes of Health > URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ > > Phone: 301-402-8103 > Address: > Advanced Technology Center, > 8717 Grovemont Circle > Gaithersburg, MD 20877 >
ADD REPLYlink written 10.9 years ago by Rafael A. Irizarry2.3k
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