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 journalArticle

2 Citations (Scopus)

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.

Original languageEnglish
JournalComputer Methods and Programs in Biomedicine
DOIs
Publication statusAccepted/In press - 2018 Jan 1

Fingerprint

Chinese Traditional Medicine
Transcriptome
Gene expression
Medicine
Drug Repositioning
Data Mining
Bioinformatics
Computational Biology
Data mining
China
Genes

Keywords

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

ASJC Scopus subject areas

  • Software
  • Computer Science Applications
  • Health Informatics

Cite this

Exploring the molecular mechanisms of Traditional Chinese Medicine components using gene expression signatures and connectivity map. / Yoo, Minjae; Shin, Jimin; Kim, Hyunmin; Kim, Jihye; Kang, Jaewoo; Tan, Aik-Choon.

In: Computer Methods and Programs in Biomedicine, 01.01.2018.

Research output: Contribution to journalArticle

@article{06890f97d76a43eda02a626a52748d2e,
title = "Exploring the molecular mechanisms of Traditional Chinese Medicine components using gene expression signatures and connectivity map",
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.",
keywords = "Bioinformatics, Connectivity map, Gene expression signatures, Mechanisms of action, Traditional Chinese Medicine",
author = "Minjae Yoo and Jimin Shin and Hyunmin Kim and Jihye Kim and Jaewoo Kang and Aik-Choon Tan",
year = "2018",
month = "1",
day = "1",
doi = "10.1016/j.cmpb.2018.04.002",
language = "English",
journal = "Computer Methods and Programs in Biomedicine",
issn = "0169-2607",
publisher = "Elsevier Ireland Ltd",

}

TY - JOUR

T1 - Exploring the molecular mechanisms of Traditional Chinese Medicine components using gene expression signatures and connectivity map

AU - Yoo, Minjae

AU - Shin, Jimin

AU - Kim, Hyunmin

AU - Kim, Jihye

AU - Kang, Jaewoo

AU - Tan, Aik-Choon

PY - 2018/1/1

Y1 - 2018/1/1

N2 - 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.

AB - 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.

KW - Bioinformatics

KW - Connectivity map

KW - Gene expression signatures

KW - Mechanisms of action

KW - Traditional Chinese Medicine

UR - http://www.scopus.com/inward/record.url?scp=85045080802&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85045080802&partnerID=8YFLogxK

U2 - 10.1016/j.cmpb.2018.04.002

DO - 10.1016/j.cmpb.2018.04.002

M3 - Article

C2 - 29650251

AN - SCOPUS:85045080802

JO - Computer Methods and Programs in Biomedicine

JF - Computer Methods and Programs in Biomedicine

SN - 0169-2607

ER -