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

[michael watson (IAH-C)]

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 at stat.math.ethz.ch [mailto:bioconductor-bounces at 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 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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