non-parametric change-point method for differential gene expression detection非参数变点检测基因差异表达的方法.pdfVIP

Non-Parametric Change-Point Method for Differential Gene Expression Detection 1 1,3,4 1,2 3,4 1 Yao Wang , Chunguo Wu , Zhaohua Ji , Binghong Wang , Yanchun Liang * 1 Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry, College of Computer Science and Technology, Jilin University, Jilin, China, 2 Inner Mongolia Xing’an Vocational Technical College, Wulanhaote, China, 3 Business School, University of Shanghai for Science and Technology, Shanghai, China, 4 Department of Modern Physics, University of Science and Technology of China, Hefei, China Abstract Background: We proposed a non-parametric method, named Non-Parametric Change Point Statistic (NPCPS for short), by using a single equation for detecting differential gene expression (DGE) in microarray data. NPCPS is based on the change point theory to provide effective DGE detecting ability. Methodology: NPCPS used the data distribution of the normal samples as input, and detects DGE in the cancer samples by locating the change point of gene expression profile. An estimate of the change point position generated by NPCPS enables the identification of the samples containing DGE. Monte Carlo simulation and ROC study were applied to examine the detecting accuracy of NPCPS, and the experiment on real microarray data of breast cancer was carried out to compare NPCPS with other methods. Conclusions: Simulation study indicated that NPCPS was more effective for detecting DGE in cancer subset compared with five parametric methods and one non-parametric method. When there were more than 8 cancer samples containing DGE, the type I error of NPCPS was below 0.01. Experiment results showed both good accuracy and relia