After analyzing NGS data, we identified a few novel miRNAs. Now the next task is to identify the target genes of these novel candidates but most of the miRNA target prediction tools identify targets for only known miRNAs. It seems the target for novel ones have to be predicted by blast with mRNAs.
Is there is any tool available for prediction of mRNA targets of novel miRNAs.
Hello.
There are many bioinformatic tools available to predict target of microRNA.
One of the best is here: www.microrna.org where a compilation of them is available as well as a list of validated target for each microRNA when available.
The problem of the predictive software is that they produce a significant number of false positive and false negative hit. The recognition site for a microRNA is heavily influenced by the structure of the RNA and deep sequencing project are revealing that these tools are effective in around 60% of the cases.
Depending on the scope of the work, whatever computational approach needs to be complemented with significant experimental activity in multiple cellular models.
Hope that this can help!
Cristiano
Hello Velumurugan,
In addition to the website mentioned above, other tools could be:
www.targetscan.org
http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html
www.mirbase.org
To find out about the pros and cons, I would suggest you to go through the following review:
Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215-33.
However, I am not expert of this field but hope this can help you in someway...
Saurabh
In addition, you can also use RNAhybrid program (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html) just to check your novel miRNA/mRNA UTR pairing and then compare that region with Targetscan cross species alignment. Alternatively, you can download the alignment from Targetscan or get the 3'-UTRs from UCSC genome browser using table browser, align with different species and check whether your novel miRNA pairing is evolutionary conserved.
miRanda - microRNA Target Detection : http://www.rnaiweb.com/cgi-bin/web/jump.cgi?ID=51
IANA microT : http://www.rnaiweb.com/cgi-bin/web/jump.cgi?ID=48
miRacle: Server for microRNA Target Prediction incorporating RNA Secondary Structure : http://www.rnaiweb.com/cgi-bin/web/jump.cgi?ID=44
PicTar : http://www.rnaiweb.com/cgi-bin/web/jump.cgi?ID=47
RNAhybrid: http://www.rnaiweb.com/cgi-bin/web/jump.cgi?ID=50
RNA22 microRNA target detection : http://www.rnaiweb.com/cgi-bin/web/jump.cgi?ID=49
These are few target prediction tools some of them are stand alone . I hope these would help you
Dear all,
Thank you very much for all your suggestions.
With regards,
Velmurugan
Hi,
in my experience one of the best tools to analyze miRNA targets is psRNATarget: http://plantgrn.noble.org/psRNATarget/
Although is focused in plant miRNAs you can also upload as targets the transcript sequences from your organism of interests.
One of the great advantages of this tool is that it allows you to "play" with a lot of different parameters. Moreover it calculates the probability of the miRNA-target to happen using an "expectation" value.
I have never use it in other organisms but plants, but probably it could be used.
Hi,
I used DIANA microT 3.0
http://diana.cslab.ece.ntua.gr/microT/
I believe this is the site recommended by Debasish, but his link wasn't working.
Once you click on the link, go below the section for "Search for targets of a specific microRNA" and click on "OR predict for your microRNA sequence." Then, just input your sequence in FASTA format.
Here is a link to a site to use to convert to FASTA. http://genome.nci.nih.gov/tools/reformat.html
The references below give some indication of how accurate the predictions are. I validated the top target using pmirGLO assay and it worked nicely.
1. M. Maragkakis; P. Alexiou; G. L. Papadopoulos; M. Reczko; T. Dalamagas; G. Giannopoulos; G. Goumas; E. Koukis; K. Kourtis; V. A. Simossis; P. Sethupathy; T. Vergoulis; N. Koziris; T. Sellis; P. Tsanakas; A. G. Hatzigeorgiou. Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 2009, 10:295 view
2. M. Maragkakis; M. Reczko; V. A. Simossis; P. Alexiou; G. L. Papadopoulos; T. Dalamagas; G. Giannopoulos; G. Goumas; E. Koukis; K. Kourtis; T. Vergoulis; N. Koziris; T. Sellis; P. Tsanakas; A. G. Hatzigeorgiou. DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Research 2009 Jul 1; 37(Web Server issue):W273-6. view
Good luck!
Hello,
InSyBio Suite demo version in on air http://demo.insybio.com/index.php?r=site%2Flogin . Among others it includes miRNA prediction, miRNA target’s prediction and ncRNA analysis tools which present accuracy over 95%. Moreover, it allows for batch executions enabling users to analyze hundreds and thousands of sequences with a single run.
The first version of InSyBio Suite will be launched in the 1st of February.
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