Bioinformatics Advance Access originally published online on January 31, 2007
Bioinformatics 2007 23(11):1321-1330; doi:10.1093/bioinformatics/btm026
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De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
1Bioinformatics Institute, Singapore 138671 and 2NUS Graduate School for Integrative Sciences & Engineering, Centre for Life Sciences, Singapore 117456
*To whom correspondence should be addressed.
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Abstract |
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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 species-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% (5-fold cross-validation accuracy) and 0.9833 (ROC score). 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 1918 pre-miRs across 40 non-human species and 3836 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: Data sets, raw statistical results and source codes are available at http://web.bii.a-star.edu.sg/~stanley/Publications
Contact: stanley{at}bii.a-star.edu.sg; santosh{at}bii.a-star.edu.sg
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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