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Question: [biomaRt] contradicting gene information
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gravatar for Paul Theodor Pyl
6.9 years ago by
Paul Theodor Pyl80 wrote:
Hi Guys, I observed the following in a dataset I'm working on: > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > getBM( attributes = c("ensembl_gene_id", "chromosome_name", "strand", "start_position", "end_position"), filters = "ensembl_gene_id", values = c("ENSG00000002586"), mart = ensembl) ensembl_gene_id chromosome_name strand start_position end_position 1 ENSG00000002586 X 1 2609220 2659350 2 ENSG00000002586 Y 1 2559220 2609350 > sessionInfo() R version 2.14.0 Under development (unstable) (2011-07-03 r56263) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.6.2 IRanges_1.12.1 biomaRt_2.10.0 loaded via a namespace (and not attached): [1] RCurl_1.7-0 tools_2.14.0 XML_3.4-3 When I check the gene on the ensembl website ( http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapi ens;idx=Gene;end=1;q=ENSG00000002586 ) or web-interface to ensembl biomart ( http://www.ensembl.org/biomart/martview ) I get the coordinates on chromosome X only. Any idea as to what might cause this? Cheers, Paul -- Paul Theodor Pyl Predoctoral Fellow Huber Group - Genome Biology Unit EMBL Heidelberg +49 6221 387-8676
ADD COMMENTlink modified 6.9 years ago by Steve Lianoglou12k • written 6.9 years ago by Paul Theodor Pyl80
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gravatar for Steve Lianoglou
6.9 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, I'm not sure what you're real question is, so I'll try to answer some potential ones inline: > I observed the following in a dataset I'm working on: > >> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> getBM( attributes = c("ensembl_gene_id", "chromosome_name", "strand", > "start_position", "end_position"), filters = "ensembl_gene_id", values = > c("ENSG00000002586"), mart = ensembl) > ?ensembl_gene_id chromosome_name strand start_position end_position > 1 ENSG00000002586 ? ? ? ? ? ? ? X ? ? ?1 ? ? ? ?2609220 ? ? ?2659350 > 2 ENSG00000002586 ? ? ? ? ? ? ? Y ? ? ?1 ? ? ? ?2559220 ? ? ?2609350 That's because: http://en.wikipedia.org/wiki/Pseudoautosomal_region > When I check the gene on the ensembl website > ( http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sa piens;idx=Gene;end=1;q=ENSG00000002586 ) When you go to that "search result" page, click through to the gene, you will also see the Y coord for it as well. > or web-interface to ensembl biomart ( http://www.ensembl.org/biomart/martview ) > > I get the coordinates on chromosome X only. > Any idea as to what might cause this? Are you asking why biomart is choosing to only show the hit for the X chromosome and not the Y? I can't venture a guess, but let me venture a guess: * Maybe it's just a limitation of web interface? * Maybe they chose to report X over Y in this view of the query because everyone has an X, but only 1/2 of the population has a Y? Or are you asking how it's possible to be on X and Y? The answer to that is in the wikipedia link above about the pseudoautosomal regions ... HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 6.9 years ago by Steve Lianoglou12k
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