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Bioinformatics Advance Access published online on January 31, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm026
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

De Novo SVM Classification of Precursor MicroRNAs from Genomic Pseudo Hairpins Using Global and Intrinsic Folding Measures

Stanley NG Kwang Loong {dagger},{ddagger},* and Santosh K. Mishra {dagger},{ddagger}

{dagger} Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671
{ddagger} NUS Graduate School for Integrative Sciences & Engineering, Centre for Life Sciences, #05-01, 28 Medical Drive, Singapore 117456

*To whom correspondence should be addressed. Stanley NG Kwang Loong, E-mail: stanley{at}bii.a-star.edu.sg


  Abstract

Motivation: MicroRNAs (miRNAs) are small ncRNAs participating in diverse cellular and physiological processes through the post-transcriptional gene regulatory pathway. Critically associated with the miRNAs biogenesis, the hairpin structure is a necessary feature for the computational classification of novel precursor miRNAs (pre-miRs). Though many of the abundant genomic inverted repeats (pseudo hairpins) can be filtered computationally, novel specie-specific pre-miRs are likely to remain elusive.

Results: miPred is a de novo Support Vector Machine (SVM) classifier for identifying pre-miRs without relying on phylogenetic conservation. To achieve significantly higher sensitivity and specificity than existing (quasi) de novo predictors, it employs a Gaussian Radial Basis Function kernel (RBF) as a similarity measure for 29 global and intrinsic hairpin folding attributes. They characterize a pre-miR at the dinucleotide sequence, hairpin folding, non-linear statistical thermodynamics, and topological levels. Trained on 200 human pre-miRs and 400 pseudo hairpins, miPred achieves 93.50% (five-fold cross-validation accuracy) and 0.9833 (area under the ROC). Tested on the remaining 123 human pre-miRs and 246 pseudo hairpins, it reports 84.55% (sensitivity), 97.97% (specificity), and 93.50% (accuracy). Validated onto 1,918 pre-miRs across 40 non-human species and 3,836 pseudo hairpins, it yields 87.65% (92.08%), 97.75% (97.42%), and 94.38% (95.64%) for the mean (overall) sensitivity, specificity, and accuracy. Notably, A. mellifera, A. Geoffroyi, C. familiaris, E. Barr, H. Simplex virus, H. cytomegalovirus, O. aries, P. patens, R. lymphocryptovirus, Simian virus, and Z. mays are unambiguously classified with 100.00% (sensitivity) and >93.75% (specificity).

Availability: Datasets, raw statistical results, and source codes are available at http://web.bii.a-star.edu.sg/~stanley/Publications

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Charlie Hodgman

Received on July 1, 2006; revised on December 13, 2006; accepted on January 23, 2007

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