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Open Access Research article

Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study

Qi Liu12, Qian Xu2, Vincent W Zheng2, Hong Xue3, Zhiwei Cao14 and Qiang Yang2*

Author Affiliations

1 College of Life Science and Biotechnology, Tongji University, China

2 Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Hong Kong

3 Department of Biochemistry, Hong Kong University of Science and Technology, Hong Kong

4 Shanghai Center for Bioinformation Technology, China

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BMC Bioinformatics 2010, 11:181  doi:10.1186/1471-2105-11-181

Published: 10 April 2010

Abstract

Background

Gene silencing using exogenous small interfering RNAs (siRNAs) is now a widespread molecular tool for gene functional study and new-drug target identification. The key mechanism in this technique is to design efficient siRNAs that incorporated into the RNA-induced silencing complexes (RISC) to bind and interact with the mRNA targets to repress their translations to proteins. Although considerable progress has been made in the computational analysis of siRNA binding efficacy, few joint analysis of different RNAi experiments conducted under different experimental scenarios has been done in research so far, while the joint analysis is an important issue in cross-platform siRNA efficacy prediction. A collective analysis of RNAi mechanisms for different datasets and experimental conditions can often provide new clues on the design of potent siRNAs.

Results

An elegant multi-task learning paradigm for cross-platform siRNA efficacy prediction is proposed. Experimental studies were performed on a large dataset of siRNA sequences which encompass several RNAi experiments recently conducted by different research groups. By using our multi-task learning method, the synergy among different experiments is exploited and an efficient multi-task predictor for siRNA efficacy prediction is obtained. The 19 most popular biological features for siRNA according to their jointly importance in multi-task learning were ranked. Furthermore, the hypothesis is validated out that the siRNA binding efficacy on different messenger RNAs(mRNAs) have different conditional distribution, thus the multi-task learning can be conducted by viewing tasks at an "mRNA"-level rather than at the "experiment"-level. Such distribution diversity derived from siRNAs bound to different mRNAs help indicate that the properties of target mRNA have important implications on the siRNA binding efficacy.

Conclusions

The knowledge gained from our study provides useful insights on how to analyze various cross-platform RNAi data for uncovering of their complex mechanism.