Question: How to filter a list of SNPs?
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gravatar for SimonNoël
8.4 years ago by
SimonNoël450
SimonNoël450 wrote:
Hello every one. I have a really big list of SNPs from all the genome and I want to restrict that llist to SNPs that point to gene expressed in the brain. How should I procede and with wich package? Simon No??l CdeC
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ADD COMMENTlink modified 8.4 years ago by Steve Lianoglou12k • written 8.4 years ago by SimonNoël450
Answer: How to filter a list of SNPs?
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gravatar for Steve Lianoglou
8.4 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, 2011/5/13 Simon No?l <simon.noel.2 at="" ulaval.ca="">: > > ? Hello every one. ?I have a really big list of SNPs from all the genome and > ? I want to restrict that llist to SNPs that point to gene expressed in the > ? brain. ?How should I procede and with wich package? To help you get better answers, can you explain what you mean by a SNP "point[ing] to" an expressed gene? Here's an answer to a question you *might* be asking: If you are talking about filtering your SNP list to the SNPs that are in cis to genes that are expressed, I would: (1) Get the appropriate gene expression data so you can get a list of expressed genes (2) Use GenomicFeatures to build a TranscriptDb using your gene annotations of your choice (3) extend the transcripts from (2) by some (cis) distance you determine is appropriate and store in `extended.expressed.genes` (4) store your SNPs as a GRanges object (I guess set strand to "*") named `snps` (5) shorter.snp.list <- subsetByOverlaps(snps, extended.expressed.genes) (6) ... (7) publish -- 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 8.4 years ago by Steve Lianoglou12k
I can modify the question... Where can I find a complete list of all gene expressed in the brain... From that, I have a good idea of what to do. Simon No?l CdeC ________________________________________ De : Steve Lianoglou [mailinglist.honeypot at gmail.com] Date d'envoi : 13 mai 2011 17:10 ? : Simon No?l Cc : bioconductor at stat.math.ethz.ch Objet : Re: [BioC] How to filter a list of SNPs? Hi, 2011/5/13 Simon No?l <simon.noel.2 at="" ulaval.ca="">: > > Hello every one. I have a really big list of SNPs from all the genome and > I want to restrict that llist to SNPs that point to gene expressed in the > brain. How should I procede and with wich package? To help you get better answers, can you explain what you mean by a SNP "point[ing] to" an expressed gene? Here's an answer to a question you *might* be asking: If you are talking about filtering your SNP list to the SNPs that are in cis to genes that are expressed, I would: (1) Get the appropriate gene expression data so you can get a list of expressed genes (2) Use GenomicFeatures to build a TranscriptDb using your gene annotations of your choice (3) extend the transcripts from (2) by some (cis) distance you determine is appropriate and store in `extended.expressed.genes` (4) store your SNPs as a GRanges object (I guess set strand to "*") named `snps` (5) shorter.snp.list <- subsetByOverlaps(snps, extended.expressed.genes) (6) ... (7) publish -- 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 REPLYlink written 8.4 years ago by SimonNoël450
Hi, 2011/5/13 Simon No?l <simon.noel.2 at="" ulaval.ca="">: > I can modify the question... > > ?Where can I find a complete list of all gene expressed in the brain... ?From that, I have a good idea of what to do. I guess you have to further specify since the brain is a complex organ :-) Are you expecting to use something like "whole brain homogenate"? Glial cells? Are you looking at particular region of the brain? You can try looking to see if there's appropriate information in the gene expression atlas: http://www.ebi.ac.uk/gxa/ Or maybe you can search GEO or the SRA for expression data taken in an experiment from a similar condition/region you are interested in. Here's a paper that looked at rna-seq from several tissues: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcb i.1000598 I see they have cerebellum there ... -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 REPLYlink written 8.4 years ago by Steve Lianoglou12k
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