Drug-response pathway analysis methods based on network analysis

• Project/Area Number: 22300099
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: The 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: ¥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.

Research Products

• [Journal Article] Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis (2013)
  • 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) Pages: 23-23
  • DOI: 10.1186/1471-2164-14-23
  • Peer Reviewed
• [Journal Article] XiP: a computational environment to create, extend, and share workflows (2013)
  • Author(s): Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S
  • Journal Title: Bioinformatics Volume: 29(1) Pages: 137-139
  • DOI: 10.1093/bioinformatics/bts630
  • Peer Reviewed
• [Journal Article] Cell cycle gene networks are associated with melanoma prognosis (2012)
  • 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)
  • DOI: 10.1371/journal.pone.0034247
  • Peer Reviewed
• [Journal Article] Epidermal growth factor receptor tyrosine kinase defines criticalprognostic genes of stage I lung adenocarcinoma (2012)
  • Author(s): 後藤 典子
  • Journal Title: PLoS One Volume: 7
  • DOI: 10.1371/journal.pone.0043923
  • Peer Reviewed
• [Journal Article] Comprehensive pharmacogenomic pathway screening by data assimilation (2011)
  • 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
  • Peer Reviewed
• [Journal Article] Searching optimal Bayesian network structure on constraint search space:super-structure approach0 (2011)
  • 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
  • Peer Reviewed
• [Journal Article] Ontology-based instance data validation for high-quality curated biological pathways (2011)
  • Author(s): Jeong E, Nagasaki M, Ueno K, Miyano S
  • Journal Title: BMC Bioinformatics Volume: 12(Suppl 1)
  • DOI: 10.1186/1471-2105-12-s1-s8
  • Peer Reviewed
• [Journal Article] CSO validator: improving manual curation workflow for biological pathways (2011)
  • Author(s): Jeong E, Nagasaki M, Ikeda E, Saito A, Miyano S
  • Journal Title: Bioinformatics Volume: 27(17) Pages: 2471-2472
  • DOI: 10.1093/bioinformatics/btr395
  • Peer Reviewed
• [Journal Article] Systems biology model repository for macrophage pathway simulation (2011)
  • Author(s): Nagasaki M, Saito A, Fujita A, Tremmel G, Ueno K, Ikeda E, Jeong E, Miyano S
  • Journal Title: Bioinformatics. Volume: 27 (11) Pages: 1591-1593
  • DOI: 10.1093/bioinformatics/btr173
  • Peer Reviewed
• [Journal Article] 2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope (2011)
  • Author(s): Osoda T, Miyano S
  • Journal Title: J Cheminformatics Volume: 3(1) Pages: 50-50
  • DOI: 10.1186/1758-2946-3-50
  • Peer Reviewed
• [Journal Article] Noise-tolerant active learning algorithm (2011)
  • Author(s): Osoda T, Miyano S
  • Journal Title: Proc.The 2011 International Conference on Data Mining Volume: 11 Pages: 10-14
  • Peer Reviewed
• [Journal Article] SiGN-SSM: open source parallel software for estimating gene networks with state space models (2011)
  • Author(s): Tamada Y, Yamaguchi R, Imoto S, Hirose O, Yoshida R, Nagasaki M, Miyano S
  • Journal Title: Bioinformatics Volume: 27(8) Pages: 1172-1173
  • DOI: 10.1093/bioinformatics/btr078
  • Peer Reviewed
• [Journal Article] Network-based predictions and simulations by biological state space models: Search for drug mode of action. J (2010)
  • Author(s): Yamaguchi R, Imoto S, Miyano S
  • Journal Title: Computer Science and Technology Volume: 25(1) Pages: 131-153
  • DOI: 10.1007/s11390-010-9311-7
  • 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
  • Peer Reviewed
• [Journal Article] Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram (2010)
  • Author(s): Li C, Nagasaki M, Saito A, Miyano S.
  • Journal Title: BMC Systems Biology Volume: 4 Pages: 39-39
  • DOI: 10.1186/1752-0509-4-39
  • Peer Reviewed
• [Journal Article] Network-based predictions and simulations by biological state space mo dels : Search for drug mode of action (2010)
  • Author(s): Yamaguchi, R., Imoto, S., Miyan o, S.
  • Journal Title: J.Computer Science and Technology Volume: 25(1) Pages: 131-153
  • Peer Reviewed
• [Journal Article] Gene regulatory network clustering for graph layout based on microarray gene expression data (2010)
  • Author(s): Kojima, K., Imoto, S., Nagasaki, M., Miyano, S.
  • Journal Title: Genome Informatics Volume: 24 Pages: 84-95
  • Peer Reviewed
• [Journal Article] Identifying hidden confounders in gene networks by Bayesian networks (2010)
  • 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
  • Peer Reviewed
• [Journal Article] Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram (2010)
  • Author(s): Li, C., Nagasaki, M., Saito, A., Miyano, S.
  • Journal Title: BMC Systems Biology Volume: 439 Pages: 1-1
• [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
• [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
  • Invited
• [Presentation] NetworkProfiler: UncoveringCancer Heterogeneity in TranscriptomeData (2011)
  • 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
• [Presentation] NetworkProfiler : Uncovering Cancer Heterogeneity in Transcriptome Data (2011)
  • 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
• [Presentation] Identification of dissimilarities in high-dimensional gene regulatory systems by predicted discrepancies from state space model (2011)
  • 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
• [Presentation] Identification of dissimilarities in high-dimensional gene regulatory systems by predicted discrepancies from state space model (2011)
  • 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
• [Presentation] Systems Biology in Supercomputing Environment (2011)
  • 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
• [Presentation] Systems Biology in Supercomputing Environment (2011)
  • 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
• [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