Question

Mapping chromosome and nucleotide position to gene name

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Steven McKinney ▴ 310

@steven-mckinney-1754

Last seen 10.3 years ago

Hi all, >From the output of a custom HMM routine, I have data showing chromosome number and nucleotide position, but no associated gene name or database identifier. e.g. > logRiList[[1]][1:10,] chromosome position end logR state 1 1 10004 10004 0.7627 3 2 1 46844 46844 -0.1648 3 3 1 59415 59415 0.1096 3 4 1 97215 97215 0.5914 3 5 1 224176 224176 0.6766 3 6 1 227744 227744 0.7047 3 7 1 311662 311662 0.4185 3 8 1 314893 314893 0.9843 3 9 1 318309 318309 0.2642 3 10 1 320085 320085 0.7877 3 How can I map this data to RefSeq Accession number or EntrezGene ID etc. so I can get the name of the gene associated with a given chromosome and nucleotide position? So far all my searches show how to do this with e.g. Affymetrix data contained in various expressionSet etc. objects, but I need to do this from this basic data state. Any suggestions appreciated Steven McKinney, Ph.D. Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada

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ADD COMMENT • link updated 15.7 years ago by Steve Lianoglou ★ 13k • written 15.7 years ago by Steven McKinney ▴ 310

score 0 · Answer 1 · 2009-04-16

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 22 months ago

United States

Hi, On Apr 16, 2009, at 3:51 PM, Steven McKinney wrote: > Hi all, > >> From the output of a custom HMM routine, > I have data showing chromosome number and nucleotide position, > but no associated gene name or database identifier. e.g. >> logRiList[[1]][1:10,] > chromosome position end logR state > 1 1 10004 10004 0.7627 3 > 2 1 46844 46844 -0.1648 3 > 3 1 59415 59415 0.1096 3 > 4 1 97215 97215 0.5914 3 > 5 1 224176 224176 0.6766 3 > 6 1 227744 227744 0.7047 3 > 7 1 311662 311662 0.4185 3 > 8 1 314893 314893 0.9843 3 > 9 1 318309 318309 0.2642 3 > 10 1 320085 320085 0.7877 3 > > How can I map this data to RefSeq Accession number or EntrezGene ID > etc. so > I can get the name of the gene associated with a given chromosome > and nucleotide > position? I'm not sure if this is optimal, but it's quite similar to what the poster was trying to do in this thread: http://thread.gmane.org/gmane.science.biology.informatics.conductor/21 445 See Martin Morgan's response for an idea of how to take a crack at it using your organism's GTF/GFF and the IRanges package. HTH, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos

ADD COMMENT • link 15.7 years ago Steve Lianoglou ★ 13k

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Thanks Steve, The thread ideas work beautifully. Thanks also to Martin Morgan for his ideas. Best Steve McKinney > -----Original Message----- > From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] > Sent: Thursday, April 16, 2009 1:03 PM > To: Steven McKinney > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Mapping chromosome and nucleotide position to gene > name > > Hi, > > On Apr 16, 2009, at 3:51 PM, Steven McKinney wrote: > > > Hi all, > > > >> From the output of a custom HMM routine, > > I have data showing chromosome number and nucleotide position, > > but no associated gene name or database identifier. e.g. > >> logRiList[[1]][1:10,] > > chromosome position end logR state > > 1 1 10004 10004 0.7627 3 > > 2 1 46844 46844 -0.1648 3 > > 3 1 59415 59415 0.1096 3 > > 4 1 97215 97215 0.5914 3 > > 5 1 224176 224176 0.6766 3 > > 6 1 227744 227744 0.7047 3 > > 7 1 311662 311662 0.4185 3 > > 8 1 314893 314893 0.9843 3 > > 9 1 318309 318309 0.2642 3 > > 10 1 320085 320085 0.7877 3 > > > > How can I map this data to RefSeq Accession number or EntrezGene ID > > etc. so > > I can get the name of the gene associated with a given chromosome > > and nucleotide > > position? > > I'm not sure if this is optimal, but it's quite similar to what the > poster was trying to do in this thread: > > http://thread.gmane.org/gmane.science.biology.informatics.conductor/21 44 5 > > See Martin Morgan's response for an idea of how to take a crack at it > using your organism's GTF/GFF and the IRanges package. > > HTH, > > -steve > > -- > Steve Lianoglou > Graduate Student: Physiology, Biophysics and Systems Biology > Weill Medical College of Cornell University > > http://cbio.mskcc.org/~lianos > >

ADD REPLY • link 15.7 years ago Steven McKinney ▴ 310