Abstract
This paper presents our computational and measurement strategy for investigating gene networks from gene expression data using state space model and dynamic Bayesian network model with nonparametric regression. These methods are applied to gene expression data based on gene knockdowns and drug responses for generating large global maps of gene regulation which will light up the geography where drug target pathways lie down.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Affara, M., Dunmore, B., Savoie, C.J., Imoto, S., Tamada, Y., Araki, H., Charnock-Jones, D.S., Miyano, S., Print, C.: Understanding endothelial cell apoptosis: What can the transcriptome glycome and proteome reveal? Philosophical Transactions of Royal Society B 362(1484), 1469–1487 (2007)
Chickering, D.M.: Learning Bayesian networks is NP-complete. In: Fisher, D., Lenz, H.-J. (eds.) Learning from Data: Artificial Intelligence and Statistics V, pp. 121–130. Springer, Heidelberg (1996)
Friedman, N., Linial, M., Nachman, I., Pe’er, D.: Using Bayesian networks to analyze expression data. J. Comput. Biol. 7(3-4), 601–620 (2000)
Hirose, O., Yoshida, R., Imoto, S., Yamaguchi, R., Higuchi, T., Charnock-Jones, D.S., Print, C., Miyano, S.: Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics 24(7), 932–942 (2008)
Imoto, S., Goto, T., Miyano, S.: Estimation of genetic networks and functional structures between genes by using Bayesian network and nonparametric regression. In: Pacific Symposium on Biocomputing, vol. 7, pp. 175–186 (2002)
Imoto, S., Kim, S., Goto, T., Aburatani, S., Tashiro, K., Kuhara, S., Miyano, S.: Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. J. Bioinf. Comp. Biol. 1(2), 231–252 (2003)
Imoto, S., Higuchi, T., Goto, T., Tashiro, K., Kuhara, S., Miyano, S.: Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. J. Bioinf. Comp. Biol. 2(1), 77–98 (2004)
Imoto, S., Tamada, Y., Araki, H., Yasuda, K., Print, C.G., Charnock-Jones, D.S., Sanders, D., Savoie, C.J., Tashiro, K., Kuhara, S., Miyano, S.: Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles. In: Pacific Symposium on Biocomputing, vol. 11, pp. 559–571 (2006)
Kim, S., Imoto, S., Miyano, S.: Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Biosystems 75(1-3), 57–65 (2004)
Kitagawa, G., Gersch, W.: Smoothness priors analysis of time series. Springer, New York (1996)
Ott, S., Imoto, S., Miyano, S.: Finding optimal models for small gene networks. In: Pacific Symp. Biocomput., vol. 9, pp. 557–567 (2004)
Ott, S., Hansen, A., Kim, S.-Y., Miyano, S.: Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution. Bioinformatics 21(2), 227–238 (2005)
Perrier, E., Imoto, S., Miyano, S.: Finding optimal Bayesian network given a super-structure. J. Machine Learning Research 9, 2251–2286 (2008)
Straus, D.S., Glass, C.K.: Anti-inflammatory actions of PPAR ligands: new insights on cellular and molecular mechanisms. Trends Immunol 28(12), 551–558 (2007)
Tamada, Y., Araki, H., Imoto, S., Nagasaki, M., Doi, A., Nakanishi, Y., Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D., Humphreys, S., Print, C., Charnock-Jones, D.S., Tashiro, K., Kuhara, S., Miyano, S.: Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks. In: Pacific Symposium on Biocomputing, vol. 14, pp. 251–263 (2009)
Yamaguchi, R., Imoto, S., Yamauchi, M., Nagasaki, M., Yoshida, R., Shimamura, T., Hatanaka, Y., Ueno, K., Higuchi, T., Gotoh, N., Miyano, S.: Predicting differences in gene regulatory systems by state space models. Genome Informatics 21, 101–113 (2008)
Yamaguchi, R., Yoshida, R., Imoto, S., Higuchi, T., Miyano, S.: Finding module-based gene networks with state-space models – Mining high-dimensional and short time-course gene expression data. IEEE Signal Processing Magazine 24(1), 37–46 (2007)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Miyano, S., Yamaguchi, R., Tamada, Y., Nagasaki, M., Imoto, S. (2009). Gene Networks Viewed through Two Models. In: Rajasekaran, S. (eds) Bioinformatics and Computational Biology. BICoB 2009. Lecture Notes in Computer Science(), vol 5462. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00727-9_8
Download citation
DOI: https://doi.org/10.1007/978-3-642-00727-9_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-00726-2
Online ISBN: 978-3-642-00727-9
eBook Packages: Computer ScienceComputer Science (R0)