Dear Sir/Madam
I know there are some websites giving you the target predicted for microRNA. I am a little confused about them. Can anyone has a reliable websites that is helpful to get the best target for microRNAS?
BEST REGARDS
PhD student SEVAN
Hi,
There are two things, one is Target prediction databases which provides information on targets collected from high throughput data screening and then further validated. In this place, you will get predicted targets, that you can analysis with your conditions and make a story. It is also suggested to use 2-4 such databases and then select the target.
While another is target prediction tools that work somewhat on algorithms, so different algorithms to identify the predicted targets. In this, you can predict even if in the database, it's not given, there all principle relies on seed sequence match.
Also, there are some websites are which provide collective results of two to four such websites.
1. Target Prediction database: TargetSCAN, miRDB, DIANA-microT, miRanada, PicTar, PITA, microT-CDS
2. Target prediction tool: miRmap
3. Collective websites: miRSystem, CSmiRTAR
Regards
Saurabh
One more helpful site : GSEA
https://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp?collection=MIR
Prediction is sequence based.
I add this database in which you can find some validated targets
http://mirtarbase.mbc.ncctu.edu.tw/php/index.php
Consider that validated targets anyway can be cell, time, pathway-dependent
Regarding prediction tools, they give just a "predictions" so should be taken with caution when looking for targets. Reading many published papers it seems very easy to fing the target for a specific miRNa, you just type the mirNA ID and magically you have your target, unfortunaltelly is it not easy as it appears, because, usually negative results and the many trials are not published.
The different prediction tools rank putative targets based on different scores, so you end up with a list of putative targets. You have then to apply a filtering-out approach based on your experimental model.
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