[BioC] miRNA validated/predicted label

[michael watson (IAH-C)]

Check out our package CORNA, published in Bioinformatics this year:

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/6/832
http://corna.sourceforge.net/
http://www.ncbi.nlm.nih.gov/pubmed/19181683

Thanks
Mick

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
mauede at alice.it
Sent: 17 June 2009 15:52
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] miRNA validated/predicted label

Thank you so much for your suggestion.
The student, who extracted and handled miRNA and target genes sequences
before my take-over,  states the following:

miRNA sequences can be downloaded from:
http://microrna.sanger.ac.uk/sequences/

Gene sequences can be download from:   http://www.ensembl.org/index.html

I see that such data can be downloaded in Fasta format pretty easily and
stored into a text file that I can manipulate through 
an R script. 
The real problem for me (I am a newbie in this research field) is to
know which miRNAs match which genes.
The matching information can come from Biology experiments which mark
the pair (miRNA, gene) as "validated".
The matching information can also come from computational predictions
which mark the pair as "predicted".
The two sets above have a non-null intersection. The goal of  our
project  is to maximize such an intersection, 
but also to increase the subset of the "predicted", not  yet
"validated", to help with Bilogists' experiments.

In short, the label "predicted", "validated", or "none of the two
cases", is very important to us.
I cannot retrieve such information in the files dowloaded from
http://microrna.sanger.ac.uk/sequences/ and 
http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl
Maybe it's just my ignorance in this field that prevents me from reading
out the information..
Anyway, also the student, who preceded me, experienced the same problem.
To overcome ths hurdle he wrote 
a python script that downloads some HTML pages  from
http://mirecords.umn.edu/miRecords/  where the 
label "validated" and /or "predicted" is attached to the respective
identifiers of the pair  miRNA <--> target gene.

Since I am familiar with R, I am not with python, I wonder whether there
exist a s/w interface  to access miRecords, which is callable from R 
scripts. ..... unless such pairs-link can somehow  be retrieved from the
dowloadable Fasta files  or some other way ...

Regards,
Maura E





tutti i telefonini TIM!


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