title: Predicting A-to-I RNA editing by feature selection and random forest.
abstract: RNA editing is a post-transcriptional RNA process that provides RNA and protein complexity for regulating gene expression in eukaryotes. It is challenging to predict RNA editing by computational methods. In this study, we developed a novel method to predict RNA editing based on a random forest method. A careful feature selection procedure was performed based on the Maximum Relevance Minimum Redundancy (mRMR) and Incremental Feature Selection (IFS) algorithms. Eighteen optimal features were selected from the 77 features in our dataset and used to construct a final predictor. The accuracy and MCC (Matthews correlation coefficient) values for the training dataset were 0.866 and 0.742, respectively; for the testing dataset, the accuracy and MCC were 0.876 and 0.576, respectively. The performance was higher using 18 features than all 77, suggesting that a small feature set was sufficient to achieve accurate prediction. Analysis of the 18 features was performed and may shed light on the mechanism and dominant factors of RNA editing, providing a basis for future experimental validation.
authors.affiliation: The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Shu
authors.affiliation: Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin, P.R. China.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China.
authors.forename: Xiangyin
authors.initials: X
authors.lastname: Kong
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.affiliation: Institute of Systems Biology, Shanghai University, Shanghai, P. R. China.
authors.forename: Yu-Dong
authors.initials: YD
authors.lastname: Cai
mesh_terms: D000818:Animals; D001483:Base Sequence; D003198:Computer Simulation; D003663:Decision Trees; D004330:Drosophila / Q000235:genetics; D017344:Genes, Insect; D023281:Genomics; D008957:Models, Genetic; D017393:RNA Editing; D017423:Sequence Analysis, RNA