microRNA: which genes code for a specific mirna?
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Tim Smith ★ 1.1k
@tim-smith-1532
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Hi, I wanted to know which gene encodes a particular miRNA. I tried the CORNA and microRNA packages. Although these give which miRNA targets which gene, I couldn't find which gene encodes an miRNA mapping. Is there any way that I can go about doing this (e.g. to find which gene encodes for hsa-mir-21)? many thanks [[alternative HTML version deleted]]
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@cei-abreu-goodger-4433
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Hi Tim, I don't think this is a Bioconductor specific problem. In any case, what do you mean? "hsa-mir-21" is the gene that encodes for "hsa-miR-21". What do you want to obtain? Some miRNAs are contained in protein coding transcripts, but not all... Cheers, Cei Tim Smith wrote: > Hi, > > I wanted to know which gene encodes a particular miRNA. I tried the CORNA and microRNA packages. Although these give which miRNA targets which gene, I couldn't find which gene encodes an miRNA mapping. > Is there any way that I can go about doing this (e.g. to find which gene encodes for hsa-mir-21)? > many thanks > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
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Thanks for the response. I want to map the methylation patterns to the expression for the miRNA to check for correlation between methylation and expression of the mirna. How should I go about doing this? thanks! ________________________________ From: Cei Abreu-Goodger <cei@ebi.ac.uk> Cc: bioc <bioconductor@stat.math.ethz.ch> Sent: Thu, March 18, 2010 11:37:53 AM Subject: Re: [BioC] microRNA: which genes code for a specific mirna? Hi Tim, I don't think this is a Bioconductor specific problem. In any case, what do you mean? "hsa-mir-21" is the gene that encodes for "hsa-miR-21". What do you want to obtain? Some miRNAs are contained in protein coding transcripts, but not all... Cheers, Cei Tim Smith wrote: > Hi, > > I wanted to know which gene encodes a particular miRNA. I tried the CORNA and microRNA packages. Although these give which miRNA targets which gene, I couldn't find which gene encodes an miRNA mapping. Is there any way that I can go about doing this (e.g. to find which gene encodes for hsa-mir-21)? > many thanks > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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On Thu, Mar 18, 2010 at 12:28 PM, Tim Smith <tim_smith_666 at="" yahoo.com=""> wrote: > Thanks for the response. > > I want to map the methylation patterns to the expression for the miRNA to check for correlation between methylation and expression of the mirna. How should I go about doing this? > thanks! Hi, Tim. Assuming that you have the methylation values for a set of genomic regions and a set of miRNAs with known genomic locations, you could certainly come up with some heuristic that associates a miRNA's with methylation measurements. What that heuristic should be I do not know, but it would likely be based on at least the distance from the methylation measurement to the miRNA location. Sean > ________________________________ > From: Cei Abreu-Goodger <cei at="" ebi.ac.uk=""> > > Cc: bioc <bioconductor at="" stat.math.ethz.ch=""> > Sent: Thu, March 18, 2010 11:37:53 AM > Subject: Re: [BioC] microRNA: which genes code for a specific mirna? > > Hi Tim, > > I don't think this is a Bioconductor specific problem. > > In any case, what do you mean? "hsa-mir-21" is the gene that encodes for "hsa-miR-21". What do you want to obtain? Some miRNAs are contained in protein coding transcripts, but not all... > > Cheers, > > Cei > > Tim Smith wrote: >> Hi, >> >> I wanted to know which gene encodes a particular miRNA. I tried the CORNA and microRNA packages. Although these give which miRNA targets which gene, I couldn't find which gene encodes an miRNA mapping. Is there any way that I can go about doing this (e.g. to find which gene encodes for hsa-mir-21)? >> many thanks >> >> >> ? ? ? ? ? [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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 >
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Hi Sean, How do I get the mapping of the miRNA to it's genomic location? The CORNA/microRNA gives the genomic location of the target gene, and not the miRNA itself. many thanks! ________________________________ From: Sean Davis <seandavi@gmail.com> Cc: Cei Abreu-Goodger <cei@ebi.ac.uk>; bioc <bioconductor@stat.math.ethz.ch> Sent: Thu, March 18, 2010 12:34:35 PM Subject: Re: [BioC] microRNA: which genes code for a specific mirna? > Thanks for the response. > > I want to map the methylation patterns to the expression for the miRNA to check for correlation between methylation and expression of the mirna. How should I go about doing this? > thanks! Hi, Tim. Assuming that you have the methylation values for a set of genomic regions and a set of miRNAs with known genomic locations, you could certainly come up with some heuristic that associates a miRNA's with methylation measurements. What that heuristic should be I do not know, but it would likely be based on at least the distance from the methylation measurement to the miRNA location. Sean > ________________________________ > From: Cei Abreu-Goodger <cei@ebi.ac.uk> > > Cc: bioc <bioconductor@stat.math.ethz.ch> > Sent: Thu, March 18, 2010 11:37:53 AM > Subject: Re: [BioC] microRNA: which genes code for a specific mirna? > > Hi Tim, > > I don't think this is a Bioconductor specific problem. > > In any case, what do you mean? "hsa-mir-21" is the gene that encodes for "hsa-miR-21". What do you want to obtain? Some miRNAs are contained in protein coding transcripts, but not all... > > Cheers, > > Cei > > Tim Smith wrote: >> Hi, >> >> I wanted to know which gene encodes a particular miRNA. I tried the CORNA and microRNA packages. Although these give which miRNA targets which gene, I couldn't find which gene encodes an miRNA mapping. Is there any way that I can go about doing this (e.g. to find which gene encodes for hsa-mir-21)? >> many thanks >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Hi, Tim Actually the miRNA chromosomal coordinates is available but hidden in the microRNA package. You can use the following script to fetch it: p=system.file("extdata", package="microRNA") hsChrmMat <- read.table(file.path(p, "hsa.gff"), header=FALSE) hsID <- gsub("[ID=\";]", "", hsChrmMat[, 10]) hsAcc <- gsub("[ACC=\";]", "", hsChrmMat[, 9]) ## process the file hsChrmCoord <- data.frame(ID = hsID, Accession = hsAcc, Chrm.Start = hsChrmMat[, 4], Chrm.End = hsChrmMat[, 5], Strand = hsChrmMat[, 7]) head(hsChrmCoord) Note that the "hsa.gff" file is in deed download from miRBase.org. I don't know how old the 'hsa.gff' file is in the microRNA package. If you want the latest one, you can download directly from miRBase and use the code above to read the file. Hope this helps. Chao-Jen On 03/18/10 09:44, Tim Smith wrote: > Hi Sean, > > How do I get the mapping of the miRNA to it's genomic location? The CORNA/microRNA gives the genomic location of the target gene, and not the miRNA itself. > many thanks! > > > > ________________________________ > From: Sean Davis <seandavi at="" gmail.com=""> > > Cc: Cei Abreu-Goodger <cei at="" ebi.ac.uk="">; bioc <bioconductor at="" stat.math.ethz.ch=""> > Sent: Thu, March 18, 2010 12:34:35 PM > Subject: Re: [BioC] microRNA: which genes code for a specific mirna? > > > >> Thanks for the response. >> >> I want to map the methylation patterns to the expression for the miRNA to check for correlation between methylation and expression of the mirna. How should I go about doing this? >> thanks! >> > Hi, Tim. > > Assuming that you have the methylation values for a set of genomic > regions and a set of miRNAs with known genomic locations, you could > certainly come up with some heuristic that associates a miRNA's with > methylation measurements. What that heuristic should be I do not > know, but it would likely be based on at least the distance from the > methylation measurement to the miRNA location. > > Sean > > >> ________________________________ >> From: Cei Abreu-Goodger <cei at="" ebi.ac.uk=""> >> >> Cc: bioc <bioconductor at="" stat.math.ethz.ch=""> >> Sent: Thu, March 18, 2010 11:37:53 AM >> Subject: Re: [BioC] microRNA: which genes code for a specific mirna? >> >> Hi Tim, >> >> I don't think this is a Bioconductor specific problem. >> >> In any case, what do you mean? "hsa-mir-21" is the gene that encodes for "hsa-miR-21". What do you want to obtain? Some miRNAs are contained in protein coding transcripts, but not all... >> >> Cheers, >> >> Cei >> >> Tim Smith wrote: >> >>> Hi, >>> >>> I wanted to know which gene encodes a particular miRNA. I tried the CORNA and microRNA packages. Although these give which miRNA targets which gene, I couldn't find which gene encodes an miRNA mapping. Is there any way that I can go about doing this (e.g. to find which gene encodes for hsa-mir-21)? >>> many thanks >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> >> > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >
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Go to the Sanger Centre's miRbase Tim Smith wrote: > Hi Sean, > > How do I get the mapping of the miRNA to it's genomic location? The CORNA/microRNA gives the genomic location of the target gene, and not the miRNA itself. > many thanks! > > > > ________________________________ > From: Sean Davis <seandavi at="" gmail.com=""> > > Cc: Cei Abreu-Goodger <cei at="" ebi.ac.uk="">; bioc <bioconductor at="" stat.math.ethz.ch=""> > Sent: Thu, March 18, 2010 12:34:35 PM > Subject: Re: [BioC] microRNA: which genes code for a specific mirna? > > > >> Thanks for the response. >> >> I want to map the methylation patterns to the expression for the miRNA to check for correlation between methylation and expression of the mirna. How should I go about doing this? >> thanks! >> > > Hi, Tim. > > Assuming that you have the methylation values for a set of genomic > regions and a set of miRNAs with known genomic locations, you could > certainly come up with some heuristic that associates a miRNA's with > methylation measurements. What that heuristic should be I do not > know, but it would likely be based on at least the distance from the > methylation measurement to the miRNA location. > > Sean > > >> ________________________________ >> From: Cei Abreu-Goodger <cei at="" ebi.ac.uk=""> >> >> Cc: bioc <bioconductor at="" stat.math.ethz.ch=""> >> Sent: Thu, March 18, 2010 11:37:53 AM >> Subject: Re: [BioC] microRNA: which genes code for a specific mirna? >> >> Hi Tim, >> >> I don't think this is a Bioconductor specific problem. >> >> In any case, what do you mean? "hsa-mir-21" is the gene that encodes for "hsa-miR-21". What do you want to obtain? Some miRNAs are contained in protein coding transcripts, but not all... >> >> Cheers, >> >> Cei >> >> Tim Smith wrote: >> >>> Hi, >>> >>> I wanted to know which gene encodes a particular miRNA. I tried the CORNA and microRNA packages. Although these give which miRNA targets which gene, I couldn't find which gene encodes an miRNA mapping. Is there any way that I can go about doing this (e.g. to find which gene encodes for hsa-mir-21)? >>> many thanks >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> >> > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >
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Hi Tim, It's actually now based in the university of Manchester: http://www.mirbase.org/ Cheers, Cei Kevin Coombes wrote: > Go to the Sanger Centre's miRbase > > Tim Smith wrote: >> Hi Sean, >> >> How do I get the mapping of the miRNA to it's genomic location? The >> CORNA/microRNA gives the genomic location of the target gene, and not >> the miRNA itself. >> many thanks! >> >> >> >> ________________________________ >> From: Sean Davis <seandavi at="" gmail.com=""> >> >> Cc: Cei Abreu-Goodger <cei at="" ebi.ac.uk="">; bioc >> <bioconductor at="" stat.math.ethz.ch=""> >> Sent: Thu, March 18, 2010 12:34:35 PM >> Subject: Re: [BioC] microRNA: which genes code for a specific mirna? >> >> >> >>> Thanks for the response. >>> >>> I want to map the methylation patterns to the expression for the >>> miRNA to check for correlation between methylation and expression of >>> the mirna. How should I go about doing this? >>> thanks! >>> >> >> Hi, Tim. >> >> Assuming that you have the methylation values for a set of genomic >> regions and a set of miRNAs with known genomic locations, you could >> certainly come up with some heuristic that associates a miRNA's with >> methylation measurements. What that heuristic should be I do not >> know, but it would likely be based on at least the distance from the >> methylation measurement to the miRNA location. >> >> Sean >> >> >>> ________________________________ >>> From: Cei Abreu-Goodger <cei at="" ebi.ac.uk=""> >>> >>> Cc: bioc <bioconductor at="" stat.math.ethz.ch=""> >>> Sent: Thu, March 18, 2010 11:37:53 AM >>> Subject: Re: [BioC] microRNA: which genes code for a specific mirna? >>> >>> Hi Tim, >>> >>> I don't think this is a Bioconductor specific problem. >>> >>> In any case, what do you mean? "hsa-mir-21" is the gene that encodes >>> for "hsa-miR-21". What do you want to obtain? Some miRNAs are >>> contained in protein coding transcripts, but not all... >>> >>> Cheers, >>> >>> Cei >>> >>> Tim Smith wrote: >>> >>>> Hi, >>>> >>>> I wanted to know which gene encodes a particular miRNA. I tried the >>>> CORNA and microRNA packages. Although these give which miRNA targets >>>> which gene, I couldn't find which gene encodes an miRNA mapping. Is >>>> there any way that I can go about doing this (e.g. to find which >>>> gene encodes for hsa-mir-21)? >>>> many thanks >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >>> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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
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Use Biomart library(biomaRt) mart.obj <- useMart(biomart = 'ensembl', dataset = 'hsapiens_gene_ensembl') atb <- c('ensembl_gene_id', 'external_gene_id', 'external_gene_db', 'chromosome_name', 'start_position', 'end_position', 'strand') mir.locs <- getBM(attributes=atb, filters="biotype", values="miRNA", mart=mart.obj) mir.locs[1:10,] ensembl_gene_id external_gene_id external_gene_db chromosome_name start_position end_position strand 1 ENSG00000222732 AC008671.1 Clone-based (Ensembl) 5 171706206 171706319 1 2 ENSG00000207864 hsa-mir-27b miRBase 9 97847727 97847823 1 3 ENSG00000221173 AL161908.1 Clone-based (Ensembl) 9 129338809 129338909 -1 4 ENSG00000222961 AC008949.1 Clone-based (Ensembl) 5 32379501 32379581 -1 5 ENSG00000221058 AC090666.2 Clone-based (Ensembl) 18 51612956 51613026 -1 6 ENSG00000207770 hsa-mir-568 miRBase 3 114035322 114035416 -1 7 ENSG00000221232 AC012047.1 Clone-based (Ensembl) 10 77887009 77887069 -1 8 ENSG00000221549 AC002480.1 Clone-based (Ensembl) 7 22551470 22551557 -1 9 ENSG00000221748 AL049647.1 Clone-based (Ensembl) 20 19321940 19322016 1 10 ENSG00000207551 hsa-mir-608 miRBase 10 102734742 102734841 1 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Tim Smith Sent: 18 March 2010 16:45 To: Sean Davis Cc: bioc Subject: Re: [BioC] microRNA: which genes code for a specific mirna? Hi Sean, How do I get the mapping of the miRNA to it's genomic location? The CORNA/microRNA gives the genomic location of the target gene, and not the miRNA itself. many thanks! ________________________________ From: Sean Davis <seandavi@gmail.com> Cc: Cei Abreu-Goodger <cei at="" ebi.ac.uk="">; bioc <bioconductor at="" stat.math.ethz.ch=""> Sent: Thu, March 18, 2010 12:34:35 PM Subject: Re: [BioC] microRNA: which genes code for a specific mirna? > Thanks for the response. > > I want to map the methylation patterns to the expression for the miRNA to check for correlation between methylation and expression of the mirna. How should I go about doing this? > thanks! Hi, Tim. Assuming that you have the methylation values for a set of genomic regions and a set of miRNAs with known genomic locations, you could certainly come up with some heuristic that associates a miRNA's with methylation measurements. What that heuristic should be I do not know, but it would likely be based on at least the distance from the methylation measurement to the miRNA location. Sean > ________________________________ > From: Cei Abreu-Goodger <cei at="" ebi.ac.uk=""> > > Cc: bioc <bioconductor at="" stat.math.ethz.ch=""> > Sent: Thu, March 18, 2010 11:37:53 AM > Subject: Re: [BioC] microRNA: which genes code for a specific mirna? > > Hi Tim, > > I don't think this is a Bioconductor specific problem. > > In any case, what do you mean? "hsa-mir-21" is the gene that encodes for "hsa-miR-21". What do you want to obtain? Some miRNAs are contained in protein coding transcripts, but not all... > > Cheers, > > Cei > > Tim Smith wrote: >> Hi, >> >> I wanted to know which gene encodes a particular miRNA. I tried the CORNA and microRNA packages. Although these give which miRNA targets which gene, I couldn't find which gene encodes an miRNA mapping. Is there any way that I can go about doing this (e.g. to find which gene encodes for hsa-mir-21)? >> many thanks >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > [[alternative HTML version deleted]] _______________________________________________ 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
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Hi Tim, I don't think this is a Bioconductor specific problem. In any case, what do you mean? "hsa-mir-21" is the gene that encodes for "hsa-miR-21". What do you want to obtain? Some miRNAs are contained in protein coding transcripts, but not all... The genename for this miRNA is simply MIR21, see http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:31586. But in the literature generally the same name (e.g., miR-21) seems to be used for the gene, the precursor, the primary, and the mature microRNA. It might be useful to read this article for some background on microRNA metabolism if you havent done so already: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4BJK582 -F&_user=10&_coverDate=01%2F23%2F2004&_rdoc=1&_fmt=high&_orig=search&_ sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_u serid=10&md5=ab04c8721417798295b966e6af5dc599 best wishes Peter Cheers, Cei Tim Smith wrote: > Hi, > > I wanted to know which gene encodes a particular miRNA. I tried the CORNA and microRNA packages. Although these give which miRNA targets which gene, I couldn't find which gene encodes an miRNA mapping. > Is there any way that I can go about doing this (e.g. to find which gene encodes for hsa-mir-21)? > many thanks > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 _______________________________________________ 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
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> > The genename for this miRNA is simply MIR21, see http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:31586. > But in the literature generally the same name (e.g., miR-21) seems to be used for the gene, the precursor, the primary, and the mature microRNA. It might be useful to read this article for some background on microRNA metabolism if you havent done so already: Some things to point out: miRBase provides a standard nomenclature for miRNAs. Most of the microarray platforms will use miRBase identifiers for their reporters (but be sure to check the version of miRBase on which they're based). hsa-mir-21 (lowercase "r") refers to a miRNA hairpin, also called the pre-miRNA. pre-miRNAs can give rise to one or two mature products (from either arm of the hairpin). hsa-miR-21 (uppercase "R") refers to the mature microRNA, or simply miRNA, produced from one arm of the mir-21 hairpin. In this case, the non-functional product is called miR-21* (when both arms give rise to detectable miRNAs, they will usually be called -5p and -3p referring to the 5' and 3' side of the hairpin). The primary transcript, which can encode multiple microRNA hairpins, as well as a protein, is referred to as the pri-miRNA. Cheers, Cei -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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