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Information Scientific Foundations of Knowledge Discovery from Proteome Data

Research Project

Project/Area Number 15300099
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionThe University of Tokyo

Principal Investigator

MIYANO Satoru  The University of Tokyo, Institute of Medical Science, Professor, 医科学研究所, 教授 (50128104)

Co-Investigator(Kenkyū-buntansha) OHM Shinobu  The University of Tokyo, Institute of Medical Science, Associate Professor, 医科学研究所, 助教授 (20160046)
AKUTSU Tatsuya  Kyoto University, Institute for Chemical Research, Professor, 化学研究所, 教授 (90261859)
IMOTO Seiya  The University of Tokyo, Institute of Medical Science, Assistant Professor, 医科学研究所, 助手 (10345027)
BANNAI Hideo  Kyushu University, Department of Informatics, Lecturer, 大学院・システム情報学研究院, 講師 (20323644)
Project Period (FY) 2003 – 2005
Project Status Completed (Fiscal Year 2005)
Budget Amount *help
¥16,500,000 (Direct Cost: ¥16,500,000)
Fiscal Year 2005: ¥4,100,000 (Direct Cost: ¥4,100,000)
Fiscal Year 2004: ¥4,800,000 (Direct Cost: ¥4,800,000)
Fiscal Year 2003: ¥7,600,000 (Direct Cost: ¥7,600,000)
Keywordsprotein network / gene network / protein-protein interaction / protein-RNA interaction prediction / pathway modeling / simulation / タンパク質相互作用 / マイクロアレイ解析 / パスウェイシミュレーション
Research Abstract

This research developed information scientific foundations of computational knowledge discovery from proteome data which came out from the genome-wide analysis of proteins and their related information. Our contributions are classified in two subjects :
1.Inferrining protein networks
We developed a statistical and computational method for inferring and estimating gene networks by using microarray gene expression data and protein-protein interaction data. This method uses a Bayesian network method combined with nonparametric regression which employs protein-protein interaction information obtained by Y2H and MS as its prior. We also developed a computational method for estimating protein complexes by applying the principal component analysis to microarray gene expression data. Further, we constructed a model which combines Bayesian networks for gene regulatory networks and Markov networks for protein networks. With this model, more accurate protein networks can be estimated from protein-protein interaction information and microarray gene expression data.
2.Computational method for pathway modeling and simulation
We defined a new basic architecture called Hybrid Functional Petri Net with extension on which a new software tool for pathway modeling and simulation was developed. This architecture allows us to use protein subcellular localization information and protein modification information in pathway modeling. By using the literature and attached data, we constructed models of pathways including protein networks with the software tool. We interpreted and evaluated these models and demonstrated the effectiveness of this method through modeling of a apoptosis signaling pathway, a cell cycle pathway model of fission yeast, and a network around p53.

Report

(4 results)
  • 2005 Annual Research Report   Final Research Report Summary
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • Research Products

    (41 results)

All 2006 2005 2004 2003 Other

All Journal Article (34 results) Book (1 results) Publications (6 results)

  • [Journal Article] Simulation based validation of the p53 transcriptional activity with hybrid functional Petri net2006

    • Author(s)
      Doi, A., Nagasaki, M., Matsuno, H., Miyano, S.
    • Journal Title

      In Silico Biology 6(In press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] A weighted profile based method for protein-RNA interacting residue prediction2006

    • Author(s)
      Jeong, E., Miyano, S.
    • Journal Title

      Lecture Notes in Computer Science 3939

      Pages: 123-139

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [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: 1-1

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] A weighted profile based method for protein-RNA interacting residue prediction.2006

    • Author(s)
      Jeong, E., Miyano, S.
    • Journal Title

      Lecture Notes in Computer Science 3939

      Pages: 123-139

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Simulation based validation of the p53 transcriptional activity with hybrid unctional Petri net2006

    • Author(s)
      Doi, A., Nagasaki, M., Matsuno, H., Miyano, S.
    • Journal Title

      In Silico Biology 6(印刷中)(In press)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] A weighted profile based method for protein-RNA interacting residue prediction2006

    • Author(s)
      Jeong, E., Miyano, S.
    • Journal Title

      Transactions on Computational Systems Biology (印刷中)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data2005

    • Author(s)
      Nariai, N., Tamada, Y., Imoto, S., hliyano, S.
    • Journal Title

      Bioinformatics 21

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Petri net modeling of biological pathways2005

    • Author(s)
      Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.
    • Journal Title

      Proc. Algebraic Biology 1

      Pages: 19-31

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Computational modeling of biological processes with Petri net based architecture2005

    • Author(s)
      Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.
    • Journal Title

      Bioinformatics Technologies (Y. P. Chen, ed). Springer Press. -B7

      Pages: 179-243

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data2005

    • Author(s)
      Nariai, N., Tamada, Y., Imoto, S., Miyano, S.
    • Journal Title

      Bioinformatics. 21

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Petri net modeling of biological pathways.2005

    • Author(s)
      Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.
    • Journal Title

      Proc. Algebraic Biology. 1

      Pages: 19-31

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data2005

    • Author(s)
      Nariai, N., Tamada, Y., Imoto, S., Miyano, S.
    • Journal Title

      Bioinformatics 21・Suppl 2

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Gene networks : estimation, modeling and simulation2005

    • Author(s)
      Imoto, S., Matsuno, H., Miyano, S.
    • Journal Title

      Computational Systems Biology(R.Eils and A.Kriete (Eds.))(Academic Press)

      Pages: 205-228

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks2004

    • Author(s)
      Nariai, N., Kim, S., Imoto, S., Miyano, S.
    • Journal Title

      Pacific Symposium on Biocomputing 9

      Pages: 336-347

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary 2004 Annual Research Report
  • [Journal Article] A Simple Method for Inferring Strengths of Protein-Protein Interactions2004

    • Author(s)
      Hayashida, M., Ueda, N., Akutsu, T
    • Journal Title

      Genome Informatics 15(1)

      Pages: 56-68

    • NAID

      130003812081

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Constructing biological pathway models with hybrid functional Petri nets2004

    • Author(s)
      Doi, A., Fujita, S., Matsuno, H., Nagasaki, M., Miyano, S.
    • Journal Title

      In Silico Biology 4(3)

      Pages: 271-291

    • NAID

      120002828980

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Modeling and simulation of fission yeast cell cycle on hybrid functional Petri net2004

    • Author(s)
      Fujita, S., Matsui, N1., Matsuno, H., Miyano, S.
    • Journal Title

      IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences E87-A(11)

      Pages: 2919-2928

    • NAID

      110003212823

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] A versatile Petri net based architecture for modeling and simulation of complex biological processes2004

    • Author(s)
      Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.
    • Journal Title

      Genome Informatics 15(1)

      Pages: 180-197

    • NAID

      120003184321

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] A neural network method for identification of RNA-interacting residues in protein2004

    • Author(s)
      Jeong, E., Chung, I., Miyano, S.
    • Journal Title

      Genome Informatics 15(1)

      Pages: 105-116

    • NAID

      130003812085

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks.2004

    • Author(s)
      Nariai, N., Kim, S., Imoto, S., Miyano, S.
    • Journal Title

      Pacific Symposium on Biocomputing. 9

      Pages: 336-347

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] A Simple Method for Inferring Strengths of Protein-Protein Interactions.2004

    • Author(s)
      Hayashida, M., Ueda, N., Akutsu, T.
    • Journal Title

      Genome Informatics 15(1)

      Pages: 56-68

    • NAID

      130003812081

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Constructing biological pathway models with hybrid functional Petri nets.2004

    • Author(s)
      Doi, A., Fujita, S., Matsuno, H., Nagasaki, M., Miyano, S.
    • Journal Title

      In Silico Biology. 4(3)

      Pages: 271-291

    • NAID

      120002828980

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Modeling and simulation of fission yeast cell cycle on hybrid functional Petri net.2004

    • Author(s)
      Fujita, S., Matsui, M., Matsuno, H., Miyano, S.
    • Journal Title

      IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences. E87-A(11)

      Pages: 2919-2928

    • NAID

      110003212823

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] A versatile Petri net based architecture for modeling and simulation of complex biological processes.2004

    • Author(s)
      Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.
    • Journal Title

      Genome Informatics 15(1)

      Pages: 180-197

    • NAID

      120003184321

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] A neural network method for identification of RNA-interacting residues in protein.2004

    • Author(s)
      Jeong, E., Chung, I., Miyano, S.
    • Journal Title

      Genome Informatics. 15(1)

      Pages: 105-116

    • NAID

      130003812085

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Efficiently finding regulatory elements using correlation with gene expression2004

    • Author(s)
      Bannai, H., Inenaga, S., Shinohara, A., Takeda, M., Miyano, S.
    • Journal Title

      J.Bioinformatics and Computational Biology 2・2

      Pages: 273-288

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Constructing biological pathway models with hybrid functional Petri nets2004

    • Author(s)
      Doi, A., Fujita, S., Matsuno, H., Nagasaki, M., Miyano, S.
    • Journal Title

      In Silico Biology 4・3

      Pages: 271-291

    • NAID

      120002828980

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Modeling and simulation of fission yeast cell cycle on hybrid functional Petri net2004

    • Author(s)
      Fujita, S., Matsui, M., Matsuno, H., Miyano, S.
    • Journal Title

      IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences E87-A・11

      Pages: 2919-2928

    • NAID

      110003212823

    • Related Report
      2004 Annual Research Report
  • [Journal Article] A simple method for inferring strengths of protein-protein interactions2004

    • Author(s)
      Hayashida, M., Ueda, N., Akutsu, T.
    • Journal Title

      Genome Informatics 15・1

      Pages: 56-68

    • NAID

      130003812081

    • Related Report
      2004 Annual Research Report
  • [Journal Article] A neural network method for identification of RNA-interacting residues in protein2004

    • Author(s)
      Jeong, E., Chung, I., Miyano, S.
    • Journal Title

      Genome Informatics 15・1

      Pages: 105-116

    • NAID

      130003812085

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Biopathways representation and simulation on hybrid functional Petri net2003

    • Author(s)
      Matsuno, H., Tanaka, Y., Aoshima, H., Doi, A., Matsui, M., Miyano, S.
    • Journal Title

      In Silico Biology 3(3)

      Pages: 389-404

    • NAID

      120002828981

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Towards biopathway modeling and simulation2003

    • Author(s)
      Matsuno, H., Fujita, S., Doi, A., Nagasaki, M., Miyano, S.
    • Journal Title

      Lecture Notes in Computer Science 2679

      Pages: 3-22

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Biopathways representation and simulation on hybrid functional Petri net.2003

    • Author(s)
      Matsuno, H., Tanaka, Y., Aoshima, H., Doi, A., Matsui, M., Miyano, S.
    • Journal Title

      In Silico Biology. 3(3)

      Pages: 389-404

    • NAID

      120002828981

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Towards biopathway modeling and simulation.2003

    • Author(s)
      Matsuno, H., Fujita, S., Doi, A., Nagasaki, M., Miyano, S.
    • Journal Title

      Lecture Notes in Computer Science. 2679

      Pages: 3-22

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Book] Bioinformatics Technologies (Y.P. Chen, ed.) ISBN : 3-540-20873-92005

    • Author(s)
      Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.
    • Publisher
      Springer Press.
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Publications] Nariai, N., Kim, S., Imoto, S., Miyano, S.: "Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks"Pacific Symposium on Biocomputing. 9巻. 336-347 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Doi, A., Nagasaki, M., Matsuno, H., Miyano, S.: "Genomic Object Net : II. Modelling biopathways by hybrid functional Petri net with extension"Applied Bioinformatics. 2巻3号. 185-188 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Miyano, S.: "Inference, Modeling and Simulation of Gene Networks"Lecture Notes in Computer Science. 2602巻. 207-211 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Matsuno, H., Tanaka, Y., Aoshiwa, H., Doi, A., Matsui, M., Miyano, S.: "Biopathways representation and simulation on hybrid functional Petri net"In Silico Biology. 3巻3号. 389-404 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.: "Genomic Object Net : I. a platform for modeling and simulating biopathways"Applied Bioinformatics. 2巻3号. 181-184 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Matsuno, H., Fujita, S., Doi, A., Nagasaki, M., Miyano, S.: "Towards biopathway modeling and simulation"Lecture Notes in Computer Science. 2679巻. 3-22 (2003)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2016-04-21  

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