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

Minjae Yoo, Jimin Shin, Hyunmin Kim, Jihye Kim, Jaewoo Kang, Aik Choon Tan

Research output: Contribution to journalArticlepeer-review

25 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)33-40
Number of pages8
JournalComputer Methods and Programs in Biomedicine
Publication statusPublished - 2019 Jun

Bibliographical note

Publisher Copyright:
© 2018 The Authors


  • Bioinformatics
  • Connectivity map
  • Gene expression signatures
  • Mechanisms of action
  • Traditional Chinese Medicine

ASJC Scopus subject areas

  • Software
  • Computer Science Applications
  • Health Informatics


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