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Co-regulated gene module detection for time series gene expression data

Frontiers of Electrical and Electronic Engineering volume 7, pages 357–366 (2012)Cite this article

Abstract

It is important to detect interaction effect of multiple genes during certain biological process. In this paper, we proposed, from systems biology perspective, the concept of co-regulated gene module, which consists of genes that are regulated by the same regulator(s). Given a time series gene expression data, a hidden Markov modelbased Bayesian model was developed to calculate the likelihood of the observed data, assuming the co-regulated gene modules are known. We further developed a Gibbs sampling strategy that is integrated with reversible jump Markov chain Monte Carlo to obtain the posterior probabilities of the co-regulated gene modules. Simulation study validated the proposed method. When compared with two existing methods, the proposed approach significantly outperformed the conventional methods.

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Authors and Affiliations

  1. MOE Key Laboratory of Bioinformatics, Bioinformatics Division, Tsinghua National Laboratory of Information Science and Technology / Department of Automation, Tsinghua University, Beijing, 100084, China

    Wanwan Tang, Rui Li, Shao Li & Yanda Li

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  1. Wanwan Tang
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  2. Rui Li
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  3. Shao Li
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  4. Yanda Li
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Correspondence to Wanwan Tang.

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Tang, W., Li, R., Li, S. et al. Co-regulated gene module detection for time series gene expression data. Front. Electr. Electron. Eng. 7, 357–366 (2012). https://doi.org/10.1007/s11460-012-0207-x

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  • DOI: https://doi.org/10.1007/s11460-012-0207-x

Keywords

  • co-regulated gene module
  • Bayesian
  • hidden Markov model
  • Markov chain Monte Carlo