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A novel approach to select differential pathways associated with hypertrophic cardiomyopathy based on gene

Xiao-Min Chen1, Ming-Jun Feng1, Cai-Jie Shen2

  • 1Department of Cardiology, Ningbo First Hospital, Ningbo, Zhejiang 315000, P.R. China.

Molecular Medicine Reports
|June 7, 2017
PubMed

Insights

This study introduces a new gene co-expression analysis method to identify significant pathways in hypertrophic cardiomyopathy (HCM). The novel approach identified more pathways than traditional methods, potentially revealing new therapeutic targets for HCM.

Area of Science:

  • Cardiovascular Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Hypertrophic cardiomyopathy (HCM) is a complex genetic heart disease.
  • Identifying key biological pathways is crucial for understanding HCM pathogenesis and developing treatments.

Purpose of the Study:

  • To develop and validate a novel gene co-expression analysis method for identifying significant pathways in human hypertrophic cardiomyopathy (HCM).
  • To compare the efficacy of the novel co-expression method against traditional pathway enrichment analysis.

Main Methods:

  • Utilized a microarray dataset (E-GEOD-36961) for HCM patients.
  • Employed an empirical Bayes method to construct gene co-expression networks and assigned pathway weights.
  • Screened informative pathways using the Reactome database and differential pathway extraction based on a weight threshold.

Main Results:

  • Identified 1,074 informative pathways and assigned weight values.
  • Extracted 447 differential pathways, including actin folding by CCT/TRiC, purine ribonucleoside monophosphate biosynthesis, and ubiquinol biosynthesis.
  • The co-expression approach yielded a greater number of pathways compared to traditional enrichment analysis.

Conclusions:

  • The developed co-expression method is a feasible approach for predicting marker pathways in HCM.
  • Identified pathways like actin folding and purine biosynthesis may elucidate HCM molecular mechanisms.
  • These findings offer potential novel therapeutic strategies for hypertrophic cardiomyopathy.

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