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Flexible and Robust Nonlinear Statistical Modeling Based on High-Dimensional Complex Heterogeneous Data Analysis

Research Project

Project/Area Number 20680016
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Statistical science
Research InstitutionThe University of Tokyo

Principal Investigator

IMOTO Seiya  The University of Tokyo, 医科学研究所, 准教授 (10345027)

Project Period (FY) 2008 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥20,540,000 (Direct Cost: ¥15,800,000、Indirect Cost: ¥4,740,000)
Fiscal Year 2010: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2009: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2008: ¥7,930,000 (Direct Cost: ¥6,100,000、Indirect Cost: ¥1,830,000)
Keywords高次元データ解析 / 異種データ統合 / ベイズ統計 / ロバスト / 超高次元データ / ヘテロデータ / 情報統合 / ベイズモデル / 階層モデル
Research Abstract

We developed robust statistical methods for extracting valuable information from various types of high-dimensional heterogeneous data. As the results, when a subset of feature variables is defined a priori, we develop a series of statistical methods that can evaluate whether the subset has a unique distribution by comparing with background variables in the given large dataset. We also proposed a robust estimation method for large gene network from microarray gene expression data and other types of data like transcription binding sites and applied it to the analysis of cancer heterogeneity.

Report

(4 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (27 results)

All 2011 2010 2009 2008 Other

All Journal Article (17 results) (of which Peer Reviewed: 7 results) Presentation (8 results) Book (1 results) Remarks (1 results)

  • [Journal Article] Comprehensive pharmacogenomic pathway screening by data assimilation2011

    • Author(s)
      T.Hasegawa, R.Yamaguchi, M.Nagasaki, S.Imoto, S.Miyano
    • Journal Title

      LNCS (Springer-Verlag) in press.

    • Related Report
      2010 Final Research Report
  • [Journal Article] Comprehensive pharmacogenomic pathway screening by data assimilation2011

    • Author(s)
      T.Hasegawa, R.Yamaguchi, M.Nagasaki, S.Imoto, S.Miyano
    • Journal Title

      Proc.7th International Symposium on Bioinformatics Research and Applications(査読付き国際会議論文)

      Volume: (印刷中)(掲載確定)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Optimal search on clustered structural constraint for learning Bayesian network structure2010

    • Author(s)
      K.Kojima, E.Perrier, S.Imoto, S.Miyano
    • Journal Title

      Journal of Machine Learning Research 11

      Pages: 285-310

    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Journal Article] Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.2010

    • Author(s)
      T.Shimamura, S.Imoto, R.Yamaguchi, M.Nagasaki, S.Miyano
    • Journal Title

      Bioinformatics 26(8)

      Pages: 1064-1072

    • Related Report
      2010 Final Research Report
  • [Journal Article] Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues2010

    • Author(s)
      A.Niida, S.Imoto, R.Yamaguchi, M.Nagasaki, S.Miyano
    • Journal Title

      PLoS One 5(6)

    • Related Report
      2010 Final Research Report
  • [Journal Article] Model-free unsupervised gene set screening based on information enrichment in expression profiles2010

    • Author(s)
      Niida, S.Imoto, R.Yamaguchi, M.Nagasaki, A.Fujita, T.Shimamura, S.Miyano
    • Journal Title

      Bioinformatics

      Pages: 3090-3097

    • Related Report
      2010 Final Research Report
  • [Journal Article] Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning2010

    • Author(s)
      S.Kawano, T.Shimamura, A.Niida, S.Imoto, R.Yamaguchi, M.Nagasaki, R.Yoshida, C.Print, S.Miyano
    • Journal Title

      IEEE Bioinformatics and Biomedicine

      Pages: 253-258

    • Related Report
      2010 Final Research Report
  • [Journal Article] Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues2010

    • Author(s)
      A.Niida, S.Imoto, R.Yamaguchi, M.Nagasaki, S.Miyano
    • Journal Title

      PLoS One

      Volume: 5(電子ジャーナル)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Model-free unsupervised gene set screening based on information enrichment in expression profiles2010

    • Author(s)
      A.Niida, S.Imoto, R.Yamaguchi, M.Nagasaki, A.Fujita, T.Shimamura, S.Miyano
    • Journal Title

      Bioinformatics

      Volume: 26 Pages: 3090-3097

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Inferring dynamic gene networks under varying conditions for transcriptomic network comparison2010

    • Author(s)
      T.Shimamura, S.Imoto, R.Yamaguchi, M.Nagasaki, S.Miyano
    • Journal Title

      Bioinformatics 26

      Pages: 1064-1072

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Gene set-based module discovery in the breast cancer transcriptome2009

    • Author(s)
      A.Niida, A.D.Smith, S.Imoto, S.Tsutsumi, H.Aburatani, M.Q.Zhang, T.kiyama
    • Journal Title

      BMC Bioinformatics 10

      Pages: 71-71

    • Related Report
      2010 Final Research Report
  • [Journal Article] Unraveling dynamic activities of autoacine pathways that control drug-response transcriptome networks2009

    • Author(s)
      Y.Tamada, H.raki, S.Imoto, M.Nagasaki, A.Doi, Y.Nakinishi, Y.Tomiyasu, K.Yasuda, B.Dunmore, D.Sanders, S.Humphries, C.Print, D.S.Charnock-Jones, K.Tashiro, S.Kuhara, S.Miyano
    • Journal Title

      Pacific Symposium on Biocomputing 14

      Pages: 251-263

    • Related Report
      2010 Final Research Report
  • [Journal Article] A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells2009

    • Author(s)
      A.Niida, S.Imoto, M.Nagasaki, R.Yamaguchi, S.Miyano
    • Journal Title

      Genome Informatics 22

      Pages: 121-131

    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Journal Article] Gene set-based module discovery in the breast cancer transcriptome2009

    • Author(s)
      A. Niida, A.D. Smith, S. Imoto, S. Tsutsumi, H. Aburatani, M. Q. Zhang and T. Akiyama
    • Journal Title

      BMC Bioinformatics 10(電子ジャーナルのため頁なし)

      Pages: 71-71

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Unraveling dynamic activities of autoacine pathways that control drug-response transcriptome networks2009

    • Author(s)
      Y. Tamada^*, H. Araki^*, S. Imoto^* et.al. (16人中3番目, *Equqally confiibution)
    • Journal Title

      Pacific Symposium on Biocomputing 14

      Pages: 251-262

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Bayesian learning of biological pathways on genomic data assimilation2008

    • Author(s)
      R.Yoshida, M.Nagasaki, R.Yamaguchi, S.Imoto, S.Miyano, T.Higuchi
    • Journal Title

      Bioinformatics 24(22)

      Pages: 2592-2601

    • Related Report
      2010 Final Research Report
  • [Journal Article] Bayesian learning of biological pathways on genomic data assimilation2008

    • Author(s)
      R. Yoshida, M. Nagasaki, R. Yamaguchi, S. Imoto, S. Miyano, T. Higuchi
    • Journal Title

      Bioinformatics 24

      Pages: 2562-2601

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] Statistical Modeling of Dynamic Gene Networks in Cancer2010

    • Author(s)
      Seiya Imoto
    • Organizer
      Winter School in Mathematical and Computational Biology
    • Place of Presentation
      オーストラリア、クイーンズランド大学
    • Year and Date
      2010-07-08
    • Related Report
      2010 Annual Research Report
  • [Presentation] Statistical Modeling of Dynamic Gene Networks in Cancer2010

    • Author(s)
      S.Imoto
    • Organizer
      Winter School in Mathematical and Computational Biology (招待講演)
    • Place of Presentation
      University of Queensland, Australia
    • Related Report
      2010 Final Research Report
  • [Presentation] Transcriptomic Network Comparison Unravels Key Differences in Gene Regulatory Networks Characterizing Cell Conditions2010

    • Author(s)
      S.Imoto
    • Organizer
      Probability and Statistics with Applications in Systems Biology (招待講演)
    • Place of Presentation
      Taiwan
    • Related Report
      2010 Final Research Report
  • [Presentation] Statistical Inference of Gene Networks for Computational Drug Target Pathway Discovery2009

    • Author(s)
      Seiya Imoto
    • Organizer
      2009 WINTER SCHOOL IN MATHEMATICAL AND COMPUTATIONAL BIOLOGY
    • Place of Presentation
      オーストラリア、クイ-ンズランド大学、ブリスベン
    • Year and Date
      2009-07-09
    • Related Report
      2009 Annual Research Report
  • [Presentation] Computational Biomarker Identification by Analyzing Time-Course Microarray Gene Expression Data2009

    • Author(s)
      S.Imoto
    • Organizer
      International Symposium of Case Studies involving Statistics and Operations Research for Decision Making : Solving Human Problems in Business, Society, and Scientific Areas, Institute of Mathematical Statistics (招待講演)
    • Place of Presentation
      Japan
    • Related Report
      2010 Final Research Report
  • [Presentation] Statistical inference of gene networks for computational drug-target pathway discovery2009

    • Author(s)
      S.Imoto
    • Organizer
      Winter School in Mathematical and Computational Biology (招待講演)
    • Place of Presentation
      University of Queensland, Australia
    • Related Report
      2010 Final Research Report
  • [Presentation] Unraveling dynamics of biological networks towards computational drug target discovery2008

    • Author(s)
      S. Imoto
    • Organizer
      Statistical Computation and Visualization 2008
    • Place of Presentation
      Academia Sinica, Taiwan
    • Year and Date
      2008-12-03
    • Related Report
      2008 Annual Research Report
  • [Presentation] Unraveling dynamics of biological networks towards computational drug target discovery2008

    • Author(s)
      S.Imoto
    • Organizer
      Statistical Computation and Visualization 2008 (招待講演)
    • Place of Presentation
      Academia Sinica, Taiwan
    • Related Report
      2010 Final Research Report
  • [Book] Computational Drug Target Pathway Discovery : A Bayesian Network Approach. (Handbook of Computational Statistics : Statistical Bioinformatics)(in H.Lu, B.Schokop, H.Zhao (Eds.))2010

    • Author(s)
      S.Imoto, Y.Tamada, H.Araki, S.Miyano
    • Publisher
      Springer-Varlag. in press.
    • Related Report
      2010 Final Research Report
  • [Remarks] ホームページ等

    • Related Report
      2010 Final Research Report

URL: 

Published: 2008-04-01   Modified: 2016-04-21  

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