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Sequence-Based Prediction of microRNA-Binding Residues in Proteins Using Cost-Sensitive Laplacian Support Vector Machines

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2 Author(s)
Jian-Sheng Wu ; Nat. Key Lab. for Novel Software Technol., Nanjing Univ., Nanjing, China ; Zhi-Hua Zhou

The recognition of microRNA (miRNA)-binding residues in proteins is helpful to understand how miRNAs silence their target genes. It is difficult to use existing computational method to predict miRNA-binding residues in proteins due to the lack of training examples. To address this issue, unlabeled data may be exploited to help construct a computational model. Semisupervised learning deals with methods for exploiting unlabeled data in addition to labeled data automatically to improve learning performance, where no human intervention is assumed. In addition, miRNA-binding proteins almost always contain a much smaller number of binding than nonbinding residues, and cost-sensitive learning has been deemed as a good solution to the class imbalance problem. In this work, a novel model is proposed for recognizing miRNA-binding residues in proteins from sequences using a cost-sensitive extension of Laplacian support vector machines (CS-LapSVM) with a hybrid feature. The hybrid feature consists of evolutionary information of the amino acid sequence (position-specific scoring matrices), the conservation information about three biochemical properties (HKM) and mutual interaction propensities in protein-miRNA complex structures. The CS-LapSVM receives good performance with an F1 score of 26.23 + 2.55% and an AUC value of 0.805 + 0.020 superior to existing approaches for the recognition of RNA-binding residues. A web server called SARS is built and freely available for academic usage.

Published in:

Computational Biology and Bioinformatics, IEEE/ACM Transactions on  (Volume:10 ,  Issue: 3 )

Date of Publication:

May-June 2013

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