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This article is part of the supplement: Selected articles from the Tenth Asia Pacific Bioinformatics Conference (APBC 2012)

Open Access Proceedings

An estimation method for inference of gene regulatory net-work using Bayesian network with uniting of partial problems

Yukito Watanabe*, Shigeto Seno, Yoichi Takenaka and Hideo Matsuda

Author Affiliations

Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan

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BMC Genomics 2012, 13(Suppl 1):S12  doi:10.1186/1471-2164-13-S1-S12

Published: 17 January 2012

Abstract

Background

Bayesian networks (BNs) have been widely used to estimate gene regulatory networks. Many BN methods have been developed to estimate networks from microarray data. However, two serious problems reduce the effectiveness of current BN methods. The first problem is that BN-based methods require huge computational time to estimate large-scale networks. The second is that the estimated network cannot have cyclic structures, even if the actual network has such structures.

Results

In this paper, we present a novel BN-based deterministic method with reduced computational time that allows cyclic structures. Our approach generates all the combinational triplets of genes, estimates networks of the triplets by BN, and unites the networks into a single network containing all genes. This method decreases the search space of predicting gene regulatory networks without degrading the solution accuracy compared with the greedy hill climbing (GHC) method. The order of computational time is the cube of number of genes. In addition, the network estimated by our method can include cyclic structures.

Conclusions

We verified the effectiveness of the proposed method for all known gene regulatory networks and their expression profiles. The results demonstrate that this approach can predict regulatory networks with reduced computational time without degrading the solution accuracy compared with the GHC method.