how to extract promoter regions and detect motif occurrence counts?

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Edward Turner ▴ 10

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Last seen 10.2 years ago

Hi, I'm new to bioconductor. Could anyone give some hints which package(s) I should use for the following purposes: 1. Extract the promoter regions of given 100 genes with Entre ID 2. Count the occurrence of given motif in promoter region of each gene, respectively. Thanks very much for your help! Best, Chen [[alternative HTML version deleted]]

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ADD COMMENT • link updated 13.1 years ago by Steve Lianoglou ★ 13k • written 13.1 years ago by Edward Turner ▴ 10

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 21 months ago

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Hi, On Sun, Oct 23, 2011 at 12:44 PM, Edward Turner <edtuer at="" gmail.com=""> wrote: > Hi, > > ?I'm new to bioconductor. Could anyone give some hints which package(s) I > should use for the following purposes: > > 1. Extract the promoter regions of given 100 genes with Entre ID > 2. Count the occurrence of given motif in promoter region of each gene, > respectively. Get familiar with: (1) GenomicFeatures (2) GenomicRanges (3) IRanges (4) Biostrings (5) The BSgenome.*.* package for the organism you are working with. (1) You will get the location of promoters using GenomicFeatures, which you will define yourself as XX bp upstream from the transcription start site of the gene (GenomicFeatures gives you, among other things, transcription bounds). (2) The results from (1) will be returned to you in a data structure that is defined in GenomicRanges, which, in turn, are objects that rely heavily on the IRanges infrastructure (3) The biostrings + BSgenome.*.* packages will allow you to find the sequences associated with the promoter ranges you defined from (1) and look for the occurrence of patterns you are looking for in them. 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 COMMENT • link 13.1 years ago Steve Lianoglou ★ 13k

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Also, if you are not familiar with R/Bioconductor, UCSC table browser may be more straightforward to get promoter sequences, then apply a motif searching program over them. Yuan On 23 Oct 2011, at 18:22, Steve Lianoglou wrote: > Hi, > > On Sun, Oct 23, 2011 at 12:44 PM, Edward Turner <edtuer at="" gmail.com=""> > wrote: >> Hi, >> >> I'm new to bioconductor. Could anyone give some hints which >> package(s) I >> should use for the following purposes: >> >> 1. Extract the promoter regions of given 100 genes with Entre ID >> 2. Count the occurrence of given motif in promoter region of each >> gene, >> respectively. > > Get familiar with: > > (1) GenomicFeatures > (2) GenomicRanges > (3) IRanges > (4) Biostrings > (5) The BSgenome.*.* package for the organism you are working with. > > (1) You will get the location of promoters using GenomicFeatures, > which you will define yourself as XX bp upstream from the > transcription start site of the gene (GenomicFeatures gives you, among > other things, transcription bounds). > > (2) The results from (1) will be returned to you in a data structure > that is defined in GenomicRanges, which, in turn, are objects that > rely heavily on the IRanges infrastructure > > (3) The biostrings + BSgenome.*.* packages will allow you to find the > sequences associated with the promoter ranges you defined from (1) and > look for the occurrence of patterns you are looking for in them. > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 13.1 years ago Yuan Hao ▴ 240

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For motif identification, I have successfully used the cosmo library. Ivan On Sun, Oct 23, 2011 at 2:16 PM, Yuan Hao <yuan.x.hao at="" gmail.com=""> wrote: > Also, if you are not familiar with R/Bioconductor, UCSC table browser may be > more straightforward to get promoter sequences, then apply a motif searching > program over them. > > Yuan > > On 23 Oct 2011, at 18:22, Steve Lianoglou wrote: > >> Hi, >> >> On Sun, Oct 23, 2011 at 12:44 PM, Edward Turner <edtuer at="" gmail.com=""> wrote: >>> >>> Hi, >>> >>> ?I'm new to bioconductor. Could anyone give some hints which package(s) I >>> should use for the following purposes: >>> >>> 1. Extract the promoter regions of given 100 genes with Entre ID >>> 2. Count the occurrence of given motif in promoter region of each gene, >>> respectively. >> >> Get familiar with: >> >> (1) GenomicFeatures >> (2) GenomicRanges >> (3) IRanges >> (4) Biostrings >> (5) The BSgenome.*.* package for the organism you are working with. >> >> (1) You will get the location of promoters using GenomicFeatures, >> which you will define yourself as XX bp upstream from the >> transcription start site of the gene (GenomicFeatures gives you, among >> other things, transcription bounds). >> >> (2) The results from (1) will be returned to you in a data structure >> that is defined in GenomicRanges, which, in turn, are objects that >> rely heavily on the IRanges infrastructure >> >> (3) The biostrings + BSgenome.*.* packages will allow you to find the >> sequences associated with the promoter ranges you defined from (1) and >> look for the occurrence of patterns you are looking for in them. >> >> 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD REPLY • link 13.1 years ago Ivan Gregoretti ▴ 310

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