[BioC] microRNA: which genes code for a specific mirna?

[Kevin Coombes]

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
>>>
>>>
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>>
>>
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>>     
>
>
>
>       
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