Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks

S. Imoto; T. Higuchi; T. Goto; K. Tashiro; S. Kuhara; S. Miyano

doi:10.1109/CSB.2003.1227309

Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks

S. Imoto, T. Higuchi, T. Goto, K. Tashiro, S. Kuhara, S. Miyano

Systems Biology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

88 Citations (Scopus)

Abstract

We propose a statistical method for estimating a gene network based on Bayesian networks from microarray gene expression data together with biological knowledge including protein-protein interactions, protein-DNA interactions, binding site information, existing literature and so on. Unfortunately, microarray data do not contain enough information for constructing gene networks accurately in many cases. Our method adds biological knowledge to the estimation method of gene networks under a Bayesian statistical framework, and also controls the trade-off between microarray information and biological knowledge automatically. We conduct Monte Carlo simulations to show the effectiveness of the proposed method. We analyze Saccharomyces cerevisiae gene expression data as an application.

Original language	English
Title of host publication	Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	104-113
Number of pages	10
ISBN (Electronic)	0769520006, 9780769520001
DOIs	https://doi.org/10.1109/CSB.2003.1227309
Publication status	Published - 2003
Event	2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States Duration: Aug 11 2003 → Aug 14 2003

Publication series

Name	Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Other

Other	2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
Country/Territory	United States
City	Stanford
Period	8/11/03 → 8/14/03

All Science Journal Classification (ASJC) codes

Electrical and Electronic Engineering
Computer Science Applications

Access to Document

10.1109/CSB.2003.1227309

Cite this

Imoto, S., Higuchi, T., Goto, T., Tashiro, K., Kuhara, S., & Miyano, S. (2003). Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 (pp. 104-113). Article 1227309 (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CSB.2003.1227309

Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. / Imoto, S.; Higuchi, T.; Goto, T. et al.
Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 104-113 1227309 (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Imoto, S, Higuchi, T, Goto, T, Tashiro, K, Kuhara, S & Miyano, S 2003, Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. in Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003., 1227309, Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003, Institute of Electrical and Electronics Engineers Inc., pp. 104-113, 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, Stanford, United States, 8/11/03. https://doi.org/10.1109/CSB.2003.1227309

Imoto S, Higuchi T, Goto T, Tashiro K, Kuhara S, Miyano S. Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc. 2003. p. 104-113. 1227309. (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003). doi: 10.1109/CSB.2003.1227309

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AB - We propose a statistical method for estimating a gene network based on Bayesian networks from microarray gene expression data together with biological knowledge including protein-protein interactions, protein-DNA interactions, binding site information, existing literature and so on. Unfortunately, microarray data do not contain enough information for constructing gene networks accurately in many cases. Our method adds biological knowledge to the estimation method of gene networks under a Bayesian statistical framework, and also controls the trade-off between microarray information and biological knowledge automatically. We conduct Monte Carlo simulations to show the effectiveness of the proposed method. We analyze Saccharomyces cerevisiae gene expression data as an application.

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Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks

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