[BioC] microRNA: which genes code for a specific mirna?
seandavi at gmail.com
Thu Mar 18 17:34:35 CET 2010
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?
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.
> 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...
> Tim Smith wrote:
>> 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
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