Utilizing Selected Di- and Trinucleotides of siRNA to Predict RNAi Activity

• Main Authors: Ye Han, Yuanning Liu, Hao Zhang, Fei He, Chonghe Shu, Liyan Dong
• Format: Article
• Language: English
• Published: Hindawi Limited 2017-01-01
• Series: Computational and Mathematical Methods in Medicine
• Online Access: http://dx.doi.org/10.1155/2017/5043984

Small interfering RNAs (siRNAs) induce posttranscriptional gene silencing in various organisms. siRNAs targeted to different positions of the same gene show different effectiveness; hence, predicting siRNA activity is a crucial step. In this paper, we developed and evaluated a powerful tool named “siRNApred” with a new mixed feature set to predict siRNA activity. To improve the prediction accuracy, we proposed 2-3NTs as our new features. A Random Forest siRNA activity prediction model was constructed using the feature set selected by our proposed Binary Search Feature Selection (BSFS) algorithm. Experimental data demonstrated that the binding site of the Argonaute protein correlates with siRNA activity. “siRNApred” is effective for selecting active siRNAs, and the prediction results demonstrate that our method can outperform other current siRNA activity prediction methods in terms of prediction accuracy.