title: Elucidating pharmacological mechanisms of natural medicines by biclustering analysis of the gene expression profile: a case study on curcumin and Si-Wu-Tang.
abstract: Natural medicines have attracted wide attention in recent years. It is of great significance to clarify the pharmacological mechanisms of natural medicines. In prior studies, we established a method for elucidating pharmacological mechanisms of natural products contained in connectivity map (cMap), in terms of module profiles of gene expression in chemical treatments. In this study, we explore whether this methodology is applicable to dissecting the pharmacological mechanisms of natural medicines beyond the agents contained in cMap. First, the gene expression profiles of curcumin (a typical isolated natural medicine) and Si-Wu-Tang (a classic traditional Chinese medicine formula) treatments were merged with those of cMap-derived 1309 agents, respectively. Then, a biclustering analysis was performed using FABIA method to identify gene modules. The biological functions of gene modules provide preliminary insights into pharmacological mechanisms of both natural medicines. The module profile can be characterized by a binary vector, which allowed us to compare the expression profiles of natural medicines with those of cMap-derived agents. Accordingly, we predicted a series of pharmacological effects for curcumin and Si-Wu-Tang by the indications of cMap-covered drugs. Most predictions were supported by experimental observations, suggesting the potential use of this method in natural medicine dissection.
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China. qyuan@webmail.hzau.edu.cn.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Quan
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China. skylib777@gmail.com.
authors.forename: Bin
authors.initials: B
authors.lastname: Li
authors.affiliation: School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China. sunym@sdu.edu.cn.
authors.forename: You-Min
authors.initials: YM
authors.lastname: Sun
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China. zhy630@mail.hzau.edu.cn.
authors.forename: Hong-Yu
authors.initials: HY
authors.lastname: Zhang
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology*; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D003474:Curcumin / Q000494:pharmacology*; D004365:Drugs, Chinese Herbal / Q000494:pharmacology*; D006801:Humans; D059467:Transcriptome / Q000187:drug effects*
chemical_list: D000970:Antineoplastic Agents; D004365:Drugs, Chinese Herbal; C403258:si-wu-tang; D003474:Curcumin