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

[Cei Abreu-Goodger]

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]]
>>>>
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>>>
>>>
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>>>
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>>>     
>>
>>
>>
>>           [[alternative HTML version deleted]]
>>
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> 
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