The effect of regions flanking target site on siRNA potency
The effect of regions flanking target site on siRNA potency
复制标题
靶位点侧翼区域对 siRNA 效力的影响
DOI：
10.1016/j.ygeno.2013.07.009
复制
发表时间：
2013-10-01
期刊：
影响因子：
4.4
通讯作者：
Zuo, Yong-Chun
中科院分区：
文献类型：
--
作者：
Liu, Li;Li, Qian-Zhong;Zuo, Yong-Chun
For a successful RNA interference (RNAi) experiment, selecting the small interference RNA (siRNA) candidates which maximize the knock down effect of the given gene is the critical step. Although various computational approaches have been attempted, the design of efficient siRNA candidates is far from satisfactory yet. In this study, we proposed a novel feature selection algorithm of combined random forest and support vector machine to predict active siRNAs. Using a publically available dataset, we demonstrated that the predictive accuracy would be markedly improved when the context sequence features outside the target site were included. The Pearson correlation coefficient for regression is as high as 0.721, compared to 0.671, 0.668, 0.680, and 0.645, for Biopredsi, i-score, ThermoComposition21 and DSIR, respectively. It revealed that siRNA-target interaction requires appropriate sequence context not only in the target site but also in a broad region flanking the target site. (C) 2013 Elsevier Inc. All rights reserved.
