This is Raghavendra singh and i am a reseach scholar in the signal transduction and the cancer biology lab, India. Actually i am planning to repress a oncogenic protein by the miRNA and i found nearly 30 miRNA hits for the 3' UTR of the m-RNA of my interest from the MIRBASE a publuc database to screen the miRNA target. I would like to find out which one is the actual miRNA that targets my m-RNA of interest from these 30 hits. I have also checked the complimentarity of the 8 bp seed region and many miRNAs have this complimentarity too and are even conserved in many species atleast a minimum of six species. So, it has become difficult for me to sort out the exact miRNA from this 30 hits, i advice me a method or a possible technique from which i can solve my problem.

Hi Raghavendra,

You'll clearly need to do some sort of initial screening to select the most promising of the possible microRNA response elements (MRE) for more rigorous testing. I hope someone can suggest some in silico approaches for this (as I'd like to read those suggestions too!).

Once you have narrowed down the candidates, there are several ways to confirm the activity of a miRNA against a particular 3'-UTR. Some of these have been discussed in this thread:
http://www.protocol-online.org/forums/inde...showtopic=10587

I'm very curious to learn about approaches to this sort of problem -- you've many possible MRE to sort through.

Best wishes,

- Jon

Maybe you can try predictions with a couple of the other algorithms (PicTar, PITA and TargetScan are 3 of my favorites) and then pull out the ones that are predicted by all three methods. You could also check out some HITS-CLIP data here: http://ago.rockefeller.edu/index.php but it isn't very complete at the moment - only a few miRNAs are listed, and it was only done in brain (I think). The drawback is that there was some paper that said "Overall, there was only modest overlap among the six methods [computational] in the sets of miRNA-target interactions predicted." Here is that paper's PubMed ID: 19160516 so you can decide for yourself.