[BioC] miRNA and validated/predicted target genes

[michael watson (IAH-C)]

CORNA gets it's miRNA target information either from miRBase targets or microRNA.org - however, you can load any data you want into it.

The confirmed microRNA targets database I know about is Tarbase: http://diana.cslab.ece.ntua.gr/tarbase/

I'm sorry if I misread your intentions - CORNA works downstream of microRNA:gene target prediction, it relies on other software and/or databases to do that.

However, if you simply want to read data from miRBase into R, then CORNA can do that.

Thanks
Mick


-----Original Message-----
From: mauede at alice.it [mailto:mauede at alice.it]
Sent: Thu 18/06/2009 4:04 AM
To: michael watson (IAH-C); Michal Okoniewski; Wacek Kusnierczyk
Cc: bioconductor at stat.math.ethz.ch
Subject: R: [BioC] miRNA and validated/predicted target genes
 
I browsed through your paper. 
It looks like CORNA is not another pair (miRNA - target gene) prediction program like miRANDA and so on ...  ?
If I am guessing right (am I ... ?) then what is CORNA basing its miRNA -target_gene affinity score on ?

In my mind I have the three phases that miRANDA uses to score such "affinity". Phase-1 implements some empirical Biology rules, phase-2 implements free energy minimization, phase-3 implements conservation of species. Each phase is a finer screening that assigns a score to the target match. The final score is the total.

I cannot understand which criteria (empirical or computational) are at the base of CORNA assessment.
Is it a synthesis of the predictions of the many programs like miRANDA (for instance many are referred in miRecords).
How is the  (miRNA-target_gene) prediction, from computational programs like miRANDA, accounted for by CORNA ?
How is the biologists' (miRNA-target_gene) validation  accounted for by CORNA ?
I read it uses a number of statistical tests but I cannot figure out which data the statistics is applied to ... maybe because
I am not familiar with the information stored in the databases mentioned in the paper.

Thank you.
Kind regards,
Maura


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Michal
Okoniewski
Sent: 17 June 2009 15:26
To: Wacek Kusnierczyk; mauede at alice.it
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] miRNA and validated/predicted target genes




-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Wacek
Kusnierczyk
Sent: Wed 6/17/2009 4:01 PM
To: mauede at alice.it
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] miRNA and validated/predicted target genes
 
mauede at alice.it wrote:
> I posted the following question to R mailing-list and was adviced to
contact the BioConductors team.
>
> I have to find humans miRNA sequences and the correspondent validated
and/or predicted gene sequences.
> The only database I know of is  http://mirecords.umn.edu/miRecords
where all such information is accessed through a set of structured web
site  pages.
> I wonder whether R or C++  provides an interface to automatically
extract such data from miRecords or any other similar database.
>
> I would greatly appreciate any suggestion even about other databases
from where it is possible to get the same sort of data and s/w packages
that facilitate database access.
>
>   

alternatively to mirecords, you can download fasta-formatted human (and
other) mirs and targets from mirbase at sanger [1], and importing fasta
to r should be an easy task for you.  alternatively, there are database
dumps available. 

i don't know of an r/bioc package targetted specifically at a mirna
database;  it's possible that the data are not available for
programmatic access otherwise than through a bulk download (or html
parsing, if you prefer...)

vQ


[1] http://microrna.sanger.ac.uk

==================

I played with miRGen :
http://www.diana.pcbi.upenn.edu/cgi-bin/miRGen/v3/Targets.cgi#Results
(quite comprehensive, seems to include miranda and several other target
databases)
and TargetScan: http://www.targetscan.org/

but as Wacek wrote - there's no biomaRt-like interface (at least I did
not see...) but a lot of fun with html/flat file parsing instead :) 

Cheers, 
Michal 

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