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Drug-response pathway analysis methods based on network analysis

Research Project

Project/Area Number 22300099
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  東京大学, 医科学研究所, 教授 (50128104)

Co-Investigator(Kenkyū-buntansha) IMOTO Seiya  東京大学, 医科学研究所, 准教授 (10345027)
YAMAGUCHI Rui  東京大学, 医科学研究所, 講師 (90380675)
NAGASAKI Masao  東京大学, 医科学研究所, 准教授 (90396862)
Co-Investigator(Renkei-kenkyūsha) WATANABE Kenji  慶應義塾大学, 医学部, 准教授 (70191757)
GOTOH Noriko  東京大学, 医科学研究所, 特任准教授 (10251448)
Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000)
Fiscal Year 2012: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Fiscal Year 2011: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Fiscal Year 2010: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000)
Keywords遺伝子ネットワーク / 薬剤応答パスウェイ / 動的モデル / シミュレーション / パ スウェイ解析 / ベイジアンネットワーク / ペトリネット / 状態空間モデル / がん / パスウェイ解析 / ベトリネット / 薬剤応答パスウェィ / Bayesiamネットワーク
Research Abstract

We developed computational/statistical methods for inferring abstract network models from time-course or case-control gene expression data of drug-responses. We also developed a series of knowledge processing technologies for efficiently constructing and systematically validating dynamic models from the literature information on biomolecular interactions. Bayesian network and state space model are employed for the former and an extended Petri net is used for the latter.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (29 results)

All 2013 2012 2011 2010

All Journal Article (20 results) (of which Peer Reviewed: 19 results) Presentation (9 results) (of which Invited: 1 results)

  • [Journal Article] Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis2013

    • Author(s)
      Affara M, Sanders D, Araki H, Tamada Y, Dunmore B, Humphreys S, Imoto S, Savoie C, Miyano S, Kuhara S, Print C, Charnock-Jones DS
    • Journal Title

      BMC Genomics

      Volume: 14(1) Issue: 1 Pages: 23-23

    • DOI

      10.1186/1471-2164-14-23

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] XiP: a computational environment to create, extend and share workflows2013

    • Author(s)
      Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 29(1) Issue: 1 Pages: 137-139

    • DOI

      10.1093/bioinformatics/bts630

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cell cycle gene networks are associated with melanoma prognosis2012

    • Author(s)
      Wang L, Hurley D, Watkins W, Araki H, Tamada Y, Muthukaruppan A, Ranjard L, Derkac E, Imoto S, Miyano S, Crampin E, Print C
    • Journal Title

      PLoS One

      Volume: 7(4) Issue: 4 Pages: e34247-e34247

    • DOI

      10.1371/journal.pone.0034247

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma2012

    • Author(s)
      後藤 典子
    • Journal Title

      PLoS ONE

      Volume: 7 Issue: 9 Pages: e43923-e43923

    • DOI

      10.1371/journal.pone.0043923

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Comprehensive pharmacogenomic pathway screening by data assimilation2011

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

      Lecture Notes in Bioinformatics

      Volume: 6674 Pages: 160-171

    • DOI

      10.1007/978-3-642-21260-4_18

    • ISBN
      9783642212598, 9783642212604
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Searching optimal Bayesian network structure on constraint search space:super-structure approach02011

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

      LectureNotes in Computer Science

      Volume: 6797 Pages: 210-218

    • DOI

      10.1007/978-3-642-25655-4_19

    • ISBN
      9783642256547, 9783642256554
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ontology-based instance data validation for high-quality curated biological pathways2011

    • Author(s)
      Jeong E, Nagasaki M, Ueno K, Miyano S
    • Journal Title

      BMC Bioinformatics

      Volume: 12(Suppl 1) Issue: S1

    • DOI

      10.1186/1471-2105-12-s1-s8

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] CSO validator: improving manual curation workflow for biological pathways2011

    • Author(s)
      Jeong E, Nagasaki M, Ikeda E, Saito A, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 27(17) Issue: 17 Pages: 2471-2472

    • DOI

      10.1093/bioinformatics/btr395

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Systems biology model repository for macrophage pathway simulation2011

    • Author(s)
      Nagasaki M, Saito A, Fujita A, Tremmel G, Ueno K, Ikeda E, Jeong E, Miyano S
    • Journal Title

      Bioinformatics.

      Volume: 27 (11) Issue: 11 Pages: 1591-1593

    • DOI

      10.1093/bioinformatics/btr173

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] CSO validator : improving manual curation workflow for biological pathways2011

    • Author(s)
      Jeong E, Nagasaki M, Ikeda E, Saito A, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 27(17) Pages: 2471-2472

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope2011

    • Author(s)
      Osoda T, Miyano S
    • Journal Title

      J Cheminformatics

      Volume: 3(1) Issue: 1 Pages: 50-50

    • DOI

      10.1186/1758-2946-3-50

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Noise-tolerant active learning algorithm2011

    • Author(s)
      Osoda T, Miyano S
    • Journal Title

      Proc.The 2011 International Conference on Data Mining

      Volume: 11 Pages: 10-14

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] SiGN-SSM : open source parallel software for estimating gene networks with state space models2011

    • Author(s)
      Tamada Y, Yamaguchi R, Imoto S, Hirose O, Yoshida R, Nagasaki M, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 27(8) Issue: 8 Pages: 1172-1173

    • DOI

      10.1093/bioinformatics/btr078

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Network-based predictions and simulations by biological state space models: Search for drug mode of action. J2010

    • Author(s)
      Yamaguchi R, Imoto S, Miyano S
    • Journal Title

      Computer Science and Technology

      Volume: 25(1) Issue: 1 Pages: 131-153

    • DOI

      10.1007/s11390-010-9311-7

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Identifying hidden confounders in gene networks by Bayesian networks. Proc.2010

    • Author(s)
      Higashigaki T, Kojima K, Yamaguchi R, Inoue M, Imoto S, Miyano S.
    • Journal Title

      10th IEEE Bioinformatics and Bioengineering

      Pages: 168-173

    • URL

      http://doi.ieeecomputersociety.org/10.1109/BIBE.2010.35

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram2010

    • Author(s)
      Li C, Nagasaki M, Saito A, Miyano S.
    • Journal Title

      BMC Systems Biology

      Volume: 4 Issue: 1 Pages: 39-39

    • DOI

      10.1186/1752-0509-4-39

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Network-based predictions and simulations by biological state space mo dels : Search for drug mode of action2010

    • Author(s)
      Yamaguchi, R., Imoto, S., Miyan o, S.
    • Journal Title

      J.Computer Science and Technology

      Volume: 25(1) Pages: 131-153

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Gene regulatory network clustering for graph layout based on microarray gene expression data2010

    • Author(s)
      Kojima, K., Imoto, S., Nagasaki, M., Miyano, S.
    • Journal Title

      Genome Informatics

      Volume: 24 Pages: 84-95

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identifying hidden confounders in gene networks by Bayesian networks2010

    • Author(s)
      Higashigaki, T., Kojima, K., Yamaguchi, R., Inoue, M., Imoto, S., Miyano, S.
    • Journal Title

      Proc.10th IEEE Bioinformatics and Bioengineering

      Pages: 168-173

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram2010

    • Author(s)
      Li, C., Nagasaki, M., Saito, A., Miyano, S.
    • Journal Title

      BMC Systems Biology

      Volume: 439 Pages: 1-1

    • Related Report
      2010 Annual Research Report
  • [Presentation] スパコンで焙り出すがんのシステムとしての薬剤応答性と多様性2012

    • Author(s)
      宮野 悟
    • Organizer
      第71回日本癌学会学術総会
    • Place of Presentation
      札幌市教育文化会館4階K-7
    • Year and Date
      2012-09-19
    • Related Report
      2012 Final Research Report
  • [Presentation] スパコンで焙り出すがんのシステムとしての薬剤応答性と多様性2012

    • Author(s)
      宮野 悟
    • Organizer
      第71回日本癌学会学術総会
    • Place of Presentation
      札幌市教育文化会館 4階 K-7
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] NetworkProfiler: UncoveringCancer Heterogeneity in TranscriptomeData2011

    • Author(s)
      Imoto S
    • Organizer
      The 4th International Conference of the ERCIM WG on COMPUTING & STATISTICS
    • Place of Presentation
      London, UK
    • Year and Date
      2011-12-19
    • Related Report
      2012 Final Research Report
  • [Presentation] NetworkProfiler : Uncovering Cancer Heterogeneity in Transcriptome Data2011

    • Author(s)
      Imoto S
    • Organizer
      The 4th International Conference of the ERCIMWG on COMPUTING & STATISTICS
    • Place of Presentation
      London, UK(招待講演)
    • Year and Date
      2011-12-19
    • Related Report
      2011 Annual Research Report
  • [Presentation] Identification of dissimilarities in high-dimensional gene regulatory systems by predicted discrepancies from state space model2011

    • Author(s)
      Yamaguchi R
    • Organizer
      Joint Meeting of the 2011 TaipeiInternational Statistical Symposium and 7th Conference of the Asian Regional Section of the IASC
    • Place of Presentation
      Academia Sinica,Taipei,Taiwan
    • Year and Date
      2011-12-17
    • Related Report
      2012 Final Research Report
  • [Presentation] Identification of dissimilarities in high-dimensional gene regulatory systems by predicted discrepancies from state space model2011

    • Author(s)
      Yamaguchi R
    • Organizer
      Joint Meeting of the 2011 Taipei International Statistical Symposium and 7th Conference of the Asian Regional Section of the IASC
    • Place of Presentation
      Academia Sinica, Taipei, Taiwan(招待講演)
    • Year and Date
      2011-12-17
    • Related Report
      2011 Annual Research Report
  • [Presentation] Systems Biology in Supercomputing Environment2011

    • Author(s)
      Miyano S
    • Organizer
      International Workshop on Biological Processes & Petri Nets (BioPPN 2011)
    • Place of Presentation
      Thistle County Hotel, Newcastle upon Tyne, UK
    • Year and Date
      2011-06-20
    • Related Report
      2012 Final Research Report
  • [Presentation] Systems Biology in Supercomputing Environment2011

    • Author(s)
      Miyano S
    • Organizer
      International Workshop on Biolo ical Processes & Petri Nets (BioPPN 2011)
    • Place of Presentation
      Thistle County Hotel, New castle upon Tyne, UK(招待講演)
    • Year and Date
      2011-06-20
    • Related Report
      2011 Annual Research Report
  • [Presentation] スパコンで焙り出す薬剤応答遺伝子ネットワーク2010

    • Author(s)
      宮野悟
    • Organizer
      COMPUTER AIDED CHEMISTRY FORUM 2010
    • Place of Presentation
      愛知県蒲郡市ホテル竹島
    • Year and Date
      2010-10-04
    • Related Report
      2010 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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