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This article is part of the supplement: Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)

Open Access Highly Accessed Research

MTar: a computational microRNA target prediction architecture for human transcriptome

Vinod Chandra12*, Reshmi Girijadevi3, Achuthsankar S Nair1*, Sreenadhan S Pillai4 and Radhakrishna M Pillai3

Author Affiliations

1 Centre for Bioinformatics, University of Kerala, Thiruvananthapuram, India

2 Department of Computer Applications, College of Engineering, Thiruvananthapuram, India

3 Translational Cancer Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India

4 Department of Instrumentation, N.S.S. College of Engineering, Pallakkad, , India

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BMC Bioinformatics 2010, 11(Suppl 1):S2  doi:10.1186/1471-2105-11-S1-S2

Published: 18 January 2010

Abstract

Background

MicroRNAs (miRNAs) play an essential task in gene regulatory networks by inhibiting the expression of target mRNAs. As their mRNA targets are genes involved in important cell functions, there is a growing interest in identifying the relationship between miRNAs and their target mRNAs. So, there is now a imperative need to develop a computational method by which we can identify the target mRNAs of existing miRNAs. Here, we proposed an efficient machine learning model to unravel the relationship between miRNAs and their target mRNAs.

Results

We present a novel computational architecture MTar for miRNA target prediction which reports 94.5% sensitivity and 90.5% specificity. We identified 16 positional, thermodynamic and structural parameters from the wet lab proven miRNA:mRNA pairs and MTar makes use of these parameters for miRNA target identification. It incorporates an Artificial Neural Network (ANN) verifier which is trained by wet lab proven microRNA targets. A number of hitherto unknown targets of many miRNA families were located using MTar. The method identifies all three potential miRNA targets (5' seed-only, 5' dominant, and 3' canonical) whereas the existing solutions focus on 5' complementarities alone.

Conclusion

MTar, an ANN based architecture for identifying functional regulatory miRNA-mRNA interaction using predicted miRNA targets. The area of target prediction has received a new momentum with the function of a thermodynamic model incorporating target accessibility. This model incorporates sixteen structural, thermodynamic and positional features of residues in miRNA: mRNA pairs were employed to select target candidates. So our novel machine learning architecture, MTar is found to be more comprehensive than the existing methods in predicting miRNA targets, especially human transcritome.