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Exploring the molecular mechanisms of Traditional Chinese Medicine components using gene expression signatures and connectivity map

Authors
Yoo, MinjaeShin, JiminKim, HyunminKim, JihyeKang, JaewooTan, Aik Choon
Issue Date
6월-2019
Publisher
ELSEVIER IRELAND LTD
Keywords
Traditional Chinese Medicine; Mechanisms of action; Gene expression signatures; Connectivity map; Bioinformatics
Citation
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, v.174, pp.33 - 40
Indexed
SCIE
SCOPUS
Journal Title
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
Volume
174
Start Page
33
End Page
40
URI
https://scholar.korea.ac.kr/handle/2021.sw.korea/64882
DOI
10.1016/j.cmpb.2018.04.002
ISSN
0169-2607
Abstract
Background and objective: Traditional Chinese Medicine (TCM) has been practiced over thousands of years in China and other Asian countries for treating various symptoms and diseases. However, the underlying molecular mechanisms of TCM are poorly understood, partly due to the "multi-component, multi-target" nature of TCM. To uncover the molecular mechanisms of TCM, we perform comprehensive gene expression analysis using connectivity map. Methods: We interrogated gene expression signatures obtained 102 TCM components using the next generation Connectivity Map (CMap) resource. We performed systematic data mining and analysis on the mechanism of action (MoA) of these TCM components based on the CMap results. Results: We clustered the 102 TCM components into four groups based on their MoAs using next generation CMap resource. We performed gene set enrichment analysis on these components to provide additional supports for explaining these molecular mechanisms. We also provided literature evidence to validate the MoAs identified through this bioinformatics analysis. Finally, we developed the Traditional Chinese Medicine Drug Repurposing Hub (TCM Hub) - a connectivity map resource to facilitate the elucidation of TCM MoA for drug repurposing research. TCMHub is freely available in http: //tanlab.ucdenver.edu/TCMHub. Conclusions: Molecular mechanisms of TCM could be uncovered by using gene expression signatures and connectivity map. Through this analysis, we identified many of the TCM components possess diverse MoAs, this may explain the applications of TCM in treating various symptoms and diseases. (C) 2018 The Authors. Published by Elsevier B.V.
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