Estimation and simulation of gene networks for developing in silico biological networks

2009 Fiscal Year Final Research Report

• Project/Area Number: 17017008
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The University of Tokyo
• Principal Investigator: MIYANO Satoru The University of Tokyo, 医科学研究所, 教授 (50128104)
• Co-Investigator(Kenkyū-buntansha): MATSUNO Hiroshi 山口大学, 大学院・理工学研究科, 教授 (10181744) ; IMOTO Seiya 東京大学, 医科学研究所, 准教授 (10345027) ; NAGASAKI Masao 東京大学, 医科学研究所, 助教 (90396862)
• Co-Investigator(Renkei-kenkyūsha): BANNAI Hideo 九州大学, 大学院・システム情報科学研究院, 准教授 (20323644)
• Project Period (FY): 2005 – 2009
• Keywords: 遺伝子ネットワーク / システム生物学 / モデリング / シミュレーション

Research Abstract

We developed a series of computational and informatics key technologies for analyzing and understanding biological systems through data analysis and simulation. By using Bayesian network, state space model and AR model as basic concepts, we devised innovative computational methods for extracting gene networks. These methods enabled us to emboss large-scale static/dynamic gene networks from gene expression data based on large-scale gene knockdowns and drug responses. We also designed Cell System Markup Language for describing knowledge of dynamic pathways and Cell System Ontology for pathway simulation with which we developed systematic methods for analyzing and understanding biological systems.

Research Products

• [Journal Article] Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model (2009)
  • Author(s): Do, J.H., Yamaguchi, R., Miyano, S.
  • Journal Title: BMC Genomics 10 Pages: 306
• [Journal Article] A state space representation of VAR models with sparse learning for dynamic gene networks (2009)
  • Author(s): Kojima, K., Yamaguchi, R., Imoto, S., Yamauchi, M., Nagasaki, M., Yoshida, R., Shimamura, T., Ueno, K., Higuchi, T., Gotoh, N., Miyano, S.
  • Journal Title: Genome Informatics 22 Pages: 56-68
• [Journal Article] BFL: a node and edge betweenness based fast layout algorithm for large scale networks (2009)
  • Author(s): Hashimoto, T.B., Nagasaki, M., Kojima, K., Miyano, S.
  • Journal Title: BMC Bioinformatics 10 Pages: 19
• [Journal Article] Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension (2009)
  • Author(s): Li, C., Nagasaki, M., Ueno, K., Miyano, S.
  • Journal Title: BMC Systems Biology 3 Pages: 42
• [Journal Article] A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells (2009)
  • Author(s): Niida, A., Imoto, S., Nagasaki, M., Yamaguchi, R., Miyano, S.
  • Journal Title: Genome Informatics 22 Pages: 121-131
• [Journal Article] Recursive regularization for inferring gene networks from time-course gene expression profiles (2009)
  • Author(s): Shimamura, T., Imoto, S., Yamaguchi, R., Fujita, A., Nagasaki, M., Miyano, S.
  • Journal Title: BMC Systems Biology 3 Pages: 41
• [Journal Article] Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models (2008)
  • Author(s): Hirose, O., Yoshida, R., Imoto, S., Yamaguchi, R., Higuchi, T., Charnock-Jones, D.S., Print, C., Miyano, S.
  • Journal Title: Bioinformatics 24(7) Pages: 932-942
• [Journal Article] Rule-based reasoning for system dynamics in cell systems (2008)
  • Author(s): Jeong, E., Nagasaki, M., Miyano, S.
  • Journal Title: Genome Informatics 20 Pages: 25-36
• [Journal Article] Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data (2008)
  • Author(s): Kojima, K., Fujita, A., Shimamura, T., Imoto, S., Miyano, S.
  • Journal Title: Genome Informatics 20 Pages: 37-51
• [Journal Article] Fast grid layout algorithm for biological networks with sweep calculation (2008)
  • Author(s): Kojima, K., Nagasaki, M., Miyano, S.
  • Journal Title: Bioinformatics 24(12) Pages: 1433-1441
• [Journal Article] Simulation analysis for the effect of light-dark cycle on the entrainment in circadian rhythm (2008)
  • Author(s): Mito, N., Ikegami, Y., Matsuno, H., Miyano, S., Inouye, S.T.
  • Journal Title: Genome Informatics 21 Pages: 212-223
• [Journal Article] Systematic reconstruction of TRANSPATH data into Cell System Markup Language (2008)
  • Author(s): Nagasaki, M., Saito, A., Chen, L., Jeong, E., Miyano, S.
  • Journal Title: BMC Systems Biology 2 Pages: 53
• [Journal Article] ExonMiner: Web service for analysis of GeneChip exon array data (2008)
  • Author(s): Numata, K., Yoshida, R., Nagasaki, M., Saito, S., Imoto, S., Miyano, S.
  • Journal Title: BMC Bioinformatics 9 Pages: 494
• [Journal Article] Clustering with time course gene expression profiles and the mixture of state space models (2007)
  • Author(s): Hirose, O., Yoshida, R., Yamaguchi, R., Imoto, S., Higuchi, T., Miyano, S.
  • Journal Title: Genome Informatics 18 Pages: 258-266
• [Journal Article] Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway (2007)
  • Author(s): Jeong, E., Nagasaki, M., Miyano, S.
  • Journal Title: Genome Informatics 18 Pages: 225-236
• [Journal Article] Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways (2007)
  • Author(s): Jeong, E., Nagasaki, M., Saito, A., Miyano, S.
  • Journal Title: In Silico Biology 7 Pages: 0055
• [Journal Article] An efficient grid layout algorithm for biological networks utilizing various biological attributes (2007)
  • Author(s): Kojima, K., Nagasaki, M., Jeong, E., Kato, M., Miyano, S.
  • Journal Title: BMC Bioinformatics 8 Pages: 76
• [Journal Article] Modeling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets (2007)
  • Author(s): Li, C., Ge, Q. -W., Nakata, M., Matsuno, H., Miyano, S.
  • Journal Title: J. Biosciences 32 Pages: 113-125
• [Journal Article] Finding module-based gene networks with state-space models? Mining high-dimensional and short time-course gene expression data. (2007)
  • Author(s): Yamaguchi, R., Yoshida, T., Imoto, S., Higuchi, T., Miyano, S.
  • Journal Title: IEEE Signal Processing Magazine. 24(1) Pages: 37-46
• [Journal Article] Simulation based validation of the p53 transcriptional activity with hybrid functional Petri net (2006)
  • Author(s): Doi, A., Nagasaki, M., Matsuno, H., Miyano, S.
  • Journal Title: In Silico Biology 6 Pages: 0001
• [Journal Article] Structural modeling and analysis of signaling pathways based on petri nets (2006)
  • Author(s): Li, C., Suzuki, S., Ge, Q. -W., Nakata, M., Matsuno, H., Miyano, S.
  • Journal Title: J. Bioinf. Comput. Biol. 4(5) Pages: 1119-1140
• [Journal Article] A new regulatory interactions suggested by simulations for circadian genetic control mechanism in mammals (2006)
  • Author(s): Matsuno, H., Inouye, S. -T., Okitsu, Y., Fujii, Y., Miyano, S.
  • Journal Title: J. Bioinformatics and Computational Biology 4(1) Pages: 139-154
• [Journal Article] Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data (2006)
  • Author(s): Nagasaki, M., Yamaguchi, R., Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T.
  • Journal Title: Genome Informatics 17(1) Pages: 46-61
• [Journal Article] Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loops by hybrid functional Petri net with extension (2006)
  • Author(s): Saito, A., Nagasaki, M., Doi, A., Ueno, K., Miyano, S.
  • Journal Title: Genome Informatics 17(1) Pages: 100-111
• [Journal Article] Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data (2006)
  • Author(s): Tasaki, S., Nagasaki, M., Oyama, M., Hata, H., Ueno, K., Yoshida, R., Higuchi, T., Sugano, S., Miyano, S.
  • Journal Title: Genome Informatics 17(2) Pages: 226-228
• [Journal Article] ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles (2006)
  • Author(s): Yoshida, R., Higuchi, T., Imoto, S., Miyano, S.
  • Journal Title: Bioinformatics 22(12) Pages: 1538-1539
• [Journal Article] Automatic drawing of biological networks using cross cost and subcomponent data (2005)
  • Author(s): Kato, M., Nagasaki, M., Doi, A., Miyano, S.
  • Journal Title: Genome Informatics 16(2) Pages: 22-31
• [Journal Article] Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data (2005)
  • Author(s): Nariai, N., Tamada, Y., Imoto, S., Miyano, S.
  • Journal Title: Bioinformatics 21 Pages: ii206-ii212
• [Journal Article] Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution (2005)
  • Author(s): Ott, S., Hansen, A., Kim, S. -Y., Miyano, S.
  • Journal Title: Bioinformatics 21(2) Pages: 227-238
• [Journal Article] Utilizing evolutionary information and gene expression data for estimating gene networks with Bayesian network models (2005)
  • Author(s): Tamada, Y., Bannai, H., Imoto, S., Katayama, T., Kanehisa, M., Miyano, S.
  • Journal Title: J. Bioinformatics and Computational Biology 3(6) Pages: 1295-1313
• [Book] Foundations of Systems Biology (2009)
  • Author(s): Nagasaki, M., Saito, A., Doi, A., Matsuno, H., Miyano, S.
  • Total Pages: 156
  • Publisher: Springer
• [Remarks] Cell System Markup Language (CSML)
  • URL: http://www.csml.org/
• [Remarks] Petri Net Pathways
  • URL: http://genome.ib.sci.yamaguchi-u.ac.jp/~pnp/
• [Remarks] Pathway Database for Cell Illustrator
  • URL: http://genome.ib.sci.yamaguchi-u.ac.jp/~gon/index.html