miRNA & mRNA microarray data correlation - is there any software that can correlate miRNA and mRNA data? (Nov/23/2007 )
I have a quick question.... is there any software that is available to correlate miRNA and target mRNA data?
I want to set up an experiment and measure miRNAs and mRNAs that are differentially up or down regulated. My boss said that it would be a night mare trying to correlate up/down regulation miRNA with the resulting down/up regulation of mRNA. Even if I had to pick and chose a few miRNAs, it would still be an uphill task to identify its targets based on in silico and in vitro analysis. But, he is willing to give the experiment a shot if there was an easier way to correlate the miRNA-mRNA data....
Do you know of any method or software that would help me do this? I appreciate your suggestions and insights.
to my best knowledge, there is no such existing tools allowing you to do that. This needs intensive bioinformatics and statistics efforts.
First you need to obtain miRNA target prediction data (such data can be downloaded from several sources such as Sanger miRNA database predicted using miRanda). Then you need to do statistics to see if changed cDNA expression is overrepresented in genes bearing miRNA targets on their 3UTR. Many published paper have done this and found some corrections between miRNAs and their target genes.
This paper (PMID: 18026111), published online a couple of days ago may be of some use (to use it I think you need to know how to use MATLAB??).
mirnamap present many mirna expression frofile ,which may be useful to predict targets.
Thanks everyone for your answers....
Thanks miRNA man for the link to the article...it was interesting
Thanks Zany, I looked at mirnamap, but am not sure I understand what you are suggesting....