Prediction of miRNA Based on miRNA Biogenesis via One-class SVM

Chemical Research in Chinese Universities ›› 2010, Vol. 26 ›› Issue (5): 803-809.

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Prediction of miRNA Based on miRNA Biogenesis via One-class SVM

LIU Yuan-ning1,2, YAN Wen1,2, ZHANG Hao1,2*, LI Zhi4, LU Hui-jun3 and LI Xin1,2

1. College of Computer Science and Technology,
2. Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, P. R. China;
3. Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun 130012, P. R. China;
4. Changchun University of Science & Technology, Changchun 130022, P. R. China;

Received:2009-12-08 Revised:2010-01-28 Online:2010-09-25 Published:2010-11-26
Contact: ZHANG Hao. E-mail: zhangh@jlu.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China(No.60971089).

Abstract

Abstract: MicroRNAs are a class of small, single-stranded RNAs which are produced by non-protein-coding RNA genes with a length of 21—29 nt. They regulate the expression of protein-encoding genes at the post-transcriptional level and the degradation of mRNAs by base pairing to mRNAs. Mature miRNAs are processed from 60—90 nt RNA hairpin structures called pre-miRNAs. At present, most of the machine learning computational methods for pre-miRNAs prediction are based on two-class SVM and use structural information of pre-miRNA hairpins. Those methods share a common feature that all of them need a negative dataset in the training dataset and feature selection in both training and testing dataset. In order to avoid selecting false negative examples of miRNA hairpins in the training dataset which may mislead the classifiers, we presented a microRNA prediction algorithm called MirBio based on miRNAs Biogenesis which is trained only on the information of the positive miRNAs class to predict miRNAs. It can predict both pre-miRNAs and miRNAs and get a relatively satisfying result in this study.

Key words: miRNAs, Hairpin, One-class classification, miRNAs Biogenesis

LIU Yuan-ning1,2, YAN Wen1,2, ZHANG Hao1,2*, LI Zhi4, LU Hui-jun3 and LI Xin1,2. Prediction of miRNA Based on miRNA Biogenesis via One-class SVM[J]. Chemical Research in Chinese Universities, 2010, 26(5): 803-809.

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Prediction of miRNA Based on miRNA Biogenesis via One-class SVM

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