Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data

Wuming Gong, Naoko Koyano-Nakagawa, Tongbin Li, Daniel J. Garry

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


Background: Decoding the temporal control of gene expression patterns is key to the understanding of the complex mechanisms that govern developmental decisions during heart development. High-throughput methods have been employed to systematically study the dynamic and coordinated nature of cardiac differentiation at the global level with multiple dimensions. Therefore, there is a pressing need to develop a systems approach to integrate these data from individual studies and infer the dynamic regulatory networks in an unbiased fashion. Results: We developed a two-step strategy to integrate data from (1) temporal RNA-seq, (2) temporal histone modification ChIP-seq, (3) transcription factor (TF) ChIP-seq and (4) gene perturbation experiments to reconstruct the dynamic network during heart development. First, we trained a logistic regression model to predict the probability (LR score) of any base being bound by 543 TFs with known positional weight matrices. Second, four dimensions of data were combined using a time-varying dynamic Bayesian network model to infer the dynamic networks at four developmental stages in the mouse [mouse embryonic stem cells (ESCs), mesoderm (MES), cardiac progenitors (CP) and cardiomyocytes (CM)]. Our method not only infers the time-varying networks between different stages of heart development, but it also identifies the TF binding sites associated with promoter or enhancers of downstream genes. Conclusion: We report a novel method to systematically integrate multi-dimensional -omics data and reconstruct the gene regulatory networks. This method will allow one to rapidly determine the cis-modules that regulate key genes during cardiac differentiation.

Original languageEnglish (US)
Article number74
JournalBMC bioinformatics
Issue number1
StatePublished - Mar 7 2015

Bibliographical note

Funding Information:
Funding support was obtained from the National Institutes of Health (R01HL122576 and U01HL100407). We acknowledge the support from the University of Minnesota Supercomputing Institute.

Publisher Copyright:
© Gong et al.; licensee BioMed Central.


  • Cardiac differentiation
  • Data integration
  • Gene regulatory network
  • Logistic regression
  • Network inference
  • Time-varying dynamic Bayesian model


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