reordering hierarchical tree based on bilateral symmetric distance重新排序的分层树基于双边对称的距离.pdfVIP

Reordering Hierarchical Tree Based on Bilateral Symmetric Distance Minho Chae1,2, James J. Chen1,3* 1 Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, United States of America, 2 Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America, 3 Graduate Institute of Biostatistics Biostatistics Center, China Medical University, Taichung, Taiwan Abstract Background: In microarray data analysis, hierarchical clustering (HC) is often used to group samples or genes according to their gene expression profiles to study their associations. In a typical HC, nested clustering structures can be quickly identified in a tree. The relationship between objects is lost, however, because clusters rather than individual objects are compared. This results in a tree that is hard to interpret. Methodology/Principal Findings: This study proposes an ordering method, HC-SYM, which minimizes bilateral symmetric distance of two adjacent clusters in a tree so that similar objects in the clusters are located in the cluster boundaries. The performance of HC-SYM was evaluated by both supervised and unsupervised approaches and compared favourably with other ordering methods. Conclusions/Significance: The intuitive relationship between objects and flexibility of the HC-SYM method can be very helpful in the exploratory analysis of not only microarray data but also similar high-dimensional data. Citation: Chae M, Chen JJ (2011) Reordering Hierarchical Tree Based on Bilateral Symmetric Distance. PLoS ONE 6(8): e22546. doi:10.1371/journal.pone.0022546 Editor: Franca Fraternali, King’s College London, United Kingdom Received December 14, 2010; Accepted June 29, 2011; Published