[1] Wu Jiansheng, Hu Minjing, Zhou Tong, Weng Jianhong, et al. Support vector machine for prediction of siRNA silencing efficacy [J]. Journal of Southeast University (English Edition), 2006, 22 (4): 501-504. [doi:10.3969/j.issn.1003-7985.2006.04.012]
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Support vector machine for prediction of siRNA silencing efficacy(
)
基于支持向量机的siRNA降解效率预测
)Journal of Southeast University (English Edition)[ISSN:1003-7985/CN:32-1325/N]
- Volumn:
- 22
- Issue:
- 2006 4
- Page:
- 501-504
- Research Field:
- Biological Science and Medical Engineering
- Publishing date:
- 2006-12-30
Info
- Title:
- Support vector machine for prediction of siRNA silencing efficacy
- 基于支持向量机的siRNA降解效率预测
- Author(s):
- Wu Jiansheng; Hu Minjing; Zhou Tong; Weng Jianhong; Jiang Peng; Sun Xiao
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
- Keywords:
- short interfering ribonucleic acid(siRNA); support vector machine; base-base correlation; receive operating characteristic(ROC)curve
- PACS:
- Q52
- DOI:
- 10.3969/j.issn.1003-7985.2006.04.012
- Abstract:
- In order to assist the design of short interfering ribonucleic acids(siRNA), 573 non-redundant siRNAs were collected from published literatures and the relationship between siRNAs sequences and RNA interference(RNAi)effect is analyzed by a support vector machine(SVM)based algorithm relied on a base-base correlation(BBC)feature. The results show that the proposed algorithm has the highest area under curve(AUC)value(0.73)of the receive operating characteristic(ROC)curve and the greatest r value(0.43)of the Pearson’s correlation coefficient. This indicates that the proposed algorithm is better than the published algorithms on the collected datasets and that more attention should be paid to the base-base correlation information in future siRNA design.
- 为了辅助siRNA 的设计, 从已发表文献中共收集到573个siRNA的实验数据, 使用基于统计学习理论的支持向量机(SVM)方法, 提取了siRNA序列的碱基对关联性(BBC)特征, 然后使用十倍交叉验证方法, 对siRNA沉默目标基因的效率进行了预测.结果表明, 基于支持向量机, 选用多项式核作为核函数的算法具有最高的AUC 值(0.73, ROC曲线图)和最高的r值(0.43, Pearson相关系数分析), 优于以前基于打分的算法.结果说明, 在以后的siRNA 的设计中应该更多关注碱基之间的关联信息.
References:
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Memo
- Memo:
- Biographies: Wu Jiansheng(1979—), male, graduate;Sun Xiao(corresponding author), male, doctor, professor, xsun@seu.edu.cn.