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

[Chao-Jen Wong]

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