Research Article The Classification of Sini Decoction Pattern in Traditional Chinese Medicine by Gene Expression Profiling Hung-Tsu Cheng, 1,2 Chaang-Ray Chen, 3 Chia-Yang Li, 4 Chao-Ying Huang, 3 Wun-Yi Shu, 5 and Ian C. Hsu 3 1 Institute of Nano Engineering and Microsystems, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 300, Taiwan 2 Classics Chinese Medicine Clinic, Taipei 104, Taiwan 3 Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300, Taiwan 4 Department of Genome Medicine, College of Medicine and Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan 5 Institute of Statistics, National Tsing Hua University, Hsinchu 300, Taiwan Correspondence should be addressed to Ian C. Hsu; ichsu@mx.nthu.edu.tw Received 18 November 2015; Revised 21 February 2016; Accepted 10 March 2016 Academic Editor: Kamal D. Moudgil Copyright © 2016 Hung-Tsu Cheng et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. We investigated the syndromes of the Sini decoction pattern (SDP), a common ZHENG in traditional Chinese medicine (TCM). Te syndromes of SDP were correlated with various severe Yang defciency related symptoms. To obtain a common profle for SDP, we distributed questionnaires to 300 senior clinical TCM practitioners. According to the survey, we concluded 2 sets of symptoms for SDP: (1) pulse feels deep or faint and (2) reversal cold of the extremities. Twenty-four individuals from Taipei City Hospital, Linsen Chinese Medicine Branch, Taiwan, were recruited. We extracted the total mRNA of peripheral blood mononuclear cells from the 24 individuals for microarray experiments. Twelve individuals (including 6 SDP patients and 6 non-SDP individuals) were used as the training set to identify biomarkers for distinguishing the SDP and non-SDP groups. Te remaining 12 individuals were used as the test set. Te test results indicated that the gene expression profles of the identifed biomarkers could efectively distinguish the 2 groups by adopting a hierarchical clustering algorithm. Our results suggest the feasibility of using the identifed biomarkers in facilitating the diagnosis of TCM ZHENGs. Furthermore, the gene expression profles of biomarker genes could provide a molecular explanation corresponding to the ZHENG of TCM. 1. Introduction Traditional Chinese medicine (TCM) has been adopted to treat the Chinese for thousands of years on the basis of some classic Chinese medicine textbooks, including Huang Ti Nei Jing (“Te Inner Cannon of Huangti”) [1], Sh´ enn´ ong Bˇ en Cˇ ao J¯ ıng [2], and Shang Han Za Bing Lun (“Treatise on Cold Damage Disorders”) [3]. Shang Han Za Bing Lun is a Chinese medical treatise written by Zhang Zhongjing before AD 220, at the end of the Han dynasty. Te treatise is the oldest comprehensive clinical textbook in the world containing principles, methods, formulas, and medicine and is the clinical literature of TCM theory with practice. To obtain the appropriate decoction for a particular ZHENG requires a diagnostic system, namely, the Decoction ZHENG proposed in Shang Han Za Bing Lun. Trough the methods of inspection, listening, smelling, inquiry, and palpation, physi- cians collect information on patients to identify their TCM ZHENGs according to their personal experience and then treat these patients with herbs, which is called decoction. Te methods applied in TCM have been criticized as insufciently scientifc. To overcome this weakness, we conducted systems biology research to diferentiate TCM ZHENGs. Systems biology-based diagnostic principles can be used to support the relationship between TCM and current bio- medicine [4, 5]. From the perspective of gene expression Hindawi Publishing Corporation Evidence-Based Complementary and Alternative Medicine Volume 2016, Article ID 8239817, 13 pages http://dx.doi.org/10.1155/2016/8239817