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TarPmiR: a new approach for microRNA target site prediction

Ding, Jun, Li, Xiaoman, Hu, Haiyan·2016·Bioinformatics
DOI 10.1093/bioinformatics/btw318PMC PMC5018371
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Abstract

Motivation: The identification of microRNA (miRNA) target sites is fundamentally important for studying gene regulation. There are dozens of computational methods available for miRNA target site prediction. Despite their existence, we still cannot reliably identify miRNA target sites, partially due to our limited understanding of the characteristics of miRNA target sites. The recently published CLASH (crosslinking ligation and sequencing of hybrids) data provide an unprecedented opportunity to study the characteristics of miRNA target sites and improve miRNA target site prediction methods. Results: Applying four different machine learning approaches to the CLASH data, we identified seven new features of miRNA target sites. Combining these new features with those commonly used by existing miRNA target prediction algorithms, we developed an approach called TarPmiR for miRNA target site prediction. Testing on two human and one mouse non-CLASH datasets, we showed that TarPmiR predicted more than 74.2% of true miRNA target sites in each dataset. Compared with three existing approaches, we demonstrated that TarPmiR is superior to these existing approaches in terms of better recall and better precision. Availability and Implementation: The TarPmiR software is freely available at http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/. Contacts: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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Fig. 1. Features selected by four different methods
Fig. 1. Features selected by four different methodsCC BY-NC · PubMed Central

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Metadata

Authors
Ding, J., Li, X., & Hu, H.
Affiliations
  • 1 Department of Electrical Engineering and Computer Science
  • 2 Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2016-05-20
Volume
32
Issue
18
Pages
2768-2775
ISSN
  • 1367-4811
  • 1367-4803
DOI
10.1093/bioinformatics/btw318
PMC
PMC5018371
Cited by
171
References
3
Language
en
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor, 145 d)

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