EURASIP Journal on Bioinformatics and Systems Biology
Volume 2007 (2007), Article ID 71312, 14 pages
doi:10.1155/2007/71312
Research Article

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

Isabel Tienda Luna,1 Yufei Huang,2 Yufang Yin,2 Diego P. Ruiz Padillo,1 and M. Carmen Carrion Perez1

1Department of Applied Physics, University of Granada, Granada 18071, Spain
2Department of Electrical and Computer Engineering, University of Texas at San Antonio (UTSA), San Antonio, TX 78249-0669, USA

Received 1 July 2006; Revised 4 December 2006; Accepted 11 May 2007

Academic Editor: Ahmed H. Tewfik

Copyright © 2007 Isabel Tienda Luna et al. 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.

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.