EURASIP Journal on Bioinformatics and Systems Biology

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Research Article
Open Access

Uncovering Gene Regulatory Networks from Time-Series Microarray Data with Variational Bayesian Structural Expectation Maximization

  • Isabel Tienda Luna1Email author,
  • Yufei Huang2,
  • Yufang Yin2,
  • Diego P Ruiz Padillo1 and
  • M Carmen Carrion Perez1
EURASIP Journal on Bioinformatics and Systems Biology20072007:71312

https://doi.org/10.1155/2007/71312

©  Isabel Tienda Luna et al. 2007

Received: 1 July 2006

Accepted: 11 May 2007

Published: 27 June 2007

Abstract

We investigate in this paper reverse engineering of gene regulatory networks from time-series microarray data. We apply dynamic Bayesian networks (DBNs) for modeling cell cycle regulations. In developing a network inference algorithm, we focus on soft solutions that can provide a posteriori probability (APP) of network topology. In particular, we propose a variational Bayesian structural expectation maximization algorithm that can learn the posterior distribution of the network model parameters and topology jointly. We also show how the obtained APPs of the network topology can be used in a Bayesian data integration strategy to integrate two different microarray data sets. The proposed VBSEM algorithm has been tested on yeast cell cycle data sets. To evaluate the confidence of the inferred networks, we apply a moving block bootstrap method. The inferred network is validated by comparing it to the KEGG pathway map.

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Authors’ Affiliations

(1)
Department of Applied Physics, University of Granada
(2)
Department of Electrical and Computer Engineering, University of Texas at San Antonio (UTSA)

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Copyright

© Isabel Tienda Luna et al. 2007

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.