When searching for miRNA validated/experimental target gens what database do people recommend. I have been using TargetScan v 6.2, miRSearch v 3.0, miRTarBase. Recently I have been looking at DIANA TarBase v. 7.0. According their reference article
I. S. Vlachos, M. D. Paraskevopoulou, D. Karagkouni, G. Georgakilas, T. Vergoulis, I. Kanellos, I-L. Anastasopoulos, S. Maniou, K. Karathanou, D. Kalfakakou, A. Fevgas, T. Dalamagas and A. G. Hatzigeorgiou. DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucl. Acids Res. (2014)
They state that the DIANA TarBase has 9- to 250-fold more entries than any other relevant database.
My data is from a miRNA-microarray using Exiqon 7th gene sliedes and LNA thecnology.
RNA from platelets in stored platelet concentrats.
Thank you.
You can try miRecords (http://c1.accurascience.com/miRecords/). This database gives you records of miRNA-mRNA interaction from many public databases.
mirTarbase is an excellent resource for mirna targets with an excellent curative team.
miRWalk2.0 (http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/) is recently launched and upgraded version of my previous database, miRWalk which is well accepted in the miRNA research community and has been referenced in more than 470 articles within the last 3 years.
miRWalk2.0 is so far the only database provides the largest available collection of predicted and validated miRNA-target interactions with several novel and unique features. Moreover, it offers several data-sets for downloading in the two most popular, ready to use formats: Rdata and GMT files. These data-sets can be easily downloaded via the holistic.html page implemented under the Predicted Target module of miRWalk2.0.
I hope this helps.
Please feel free to contact me, if you need further information regarding miRWalk2.0.
Best wishes,
Harsh
Thank you all for your help and comments.
I think miRecords is nice web-tool with lot of information on the validation experiments, however you have to choose your miRNA of interest from a drop down list of miRNA‘s with validated target genes. That can be time consuming when you are looking at many miRNA‘s.
miRecrods was last updated 27.04.2013 and has 2705 validated records interaction miRNA-garget gene interaction. 644 miRNA´s and 1901 gens in 9 species.
miRTarbase and TarBase v 7.0 are both excellent validated target gene databases, manually curated and withhold information from experiments using NGS. miRTarbase last version 01.11.2013 has 51,460 validated interaction of 1232 miRNA and 17,520 genes from 18 species. TarBase v 7.0 (2014) has more than 500,000 interactions from 24 species.
miRWalk 2.0 lunched 02.12.2014 has about 858,750,070 interactions between 11,748 miRNAs and 308,700 genes and collects information from existing databases like miRTarbase and miRecords. You can copy paste 20 miRNA in to the search window and preform a single search for all validated target gene interactions. This feture fits nicely with my research since I have a bulk of miRNA´s that I want to look at. You can even upload a txt file with your miRNA‘s of interest.
Each new database ore version has more information than the last one.
As of now my choice is miRWalk 2.0.
Thank you all again for your help and comments.
How one can get the miRNA sequences and its 3'UTR target sequence ?
For my research i need only the sequences for validated target sites.
Any Help?
Hello, everyone :)
I have a question
In my own experience, most of the tools such as miRwalk only accept 100 genes. Is there a tool to put both miRNAs and genes lists together for the purpose of target prediction within a list?sth be flexible to work with a large list more than 100 queries?
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