Development of methods to extact kowledge from drug-stimulated gene expression time-coure compendium data

• Project/Area Number: 24700292
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Bioinformatics/Life informatics
• Research Institution: The University of Tokyo
• Principal Investigator: YAMAGUCHI Rui 東京大学, 医科学研究所, 講師 (90380675)
• Project Period (FY): 2012-04-01 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2013: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2012: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: バイオインフォマティクス / 統計的時系列モデル / 薬剤応答 / 薬剤構造 / 時系列遺伝子発現データ

Research Abstract

In this study, we investigated a statistical methodology to extract useful knowledge from gene-expression time-course compendium data of rats under multiple-drug stimulation. We studied methods to integrate heterogeneous information from drug structures and reactions of biological systems to drug stimulation and invented a method to obtain summarized features of the reactions using time-series model. Finally, we developed a method to predict the summarized biological reactions from the drug structures based on a statistical time-series model.

Research Products

• [Journal Article] Computational gene network analysis reveals TNF-induced angiogenesis (2012)
  • Author(s): Ogami K, Yamaguchi R, Imoto S, Tamada Y, Araki H, Print C, Miyano S.
  • Journal Title: BMC Systems Biology
  • Peer Reviewed
• [Journal Article] Computational gene network analysis reveals TNF-induced angiogenesis (2012)
  • Author(s): Ogami K, Yamaguchi R, Imoto S, Tamada Y, Araki H, Print C, Miyano S
  • Journal Title: BMC Systems Biology Volume: 6(Supple 2) Issue: S2
  • DOI: 10.1186/1752-0509-6-s2-s12
  • Peer Reviewed
• [Presentation] Modeling of dynamic drug effect on gene networks (2013)
  • Author(s): Maruyama Y, Yamaguchi R, Imoto S, Miyano S.
  • Organizer: The 13^<th> Annual International Workshop on Bioinformatics and Systems Biology
  • Place of Presentation: 京都大学
  • Year and Date: 2013-08-01
• [Presentation] Modeling of dynamic drug effect on gene networks (2013)
  • Author(s): Maruyama Y, Yamaguchi R, Imoto S, Miyano S
  • Organizer: The 13th Annual International Workshop on Bioinformatics and Systems Biology (IBSB2013)
  • Place of Presentation: 京都大学宇治キャンパス
• [Presentation] Computational gene network analysis reveals TNF-induced angiogenesis (2012)
  • Author(s): 尾上健太郎、山口類、井元清也、玉田嘉紀、荒木啓充、Cristin Pring、宮野悟
  • Organizer: The 23^<rd> International Conference on Genome Informatics
  • Place of Presentation: 台湾
  • Year and Date: 2012-12-12
• [Presentation] Computational gene network analysis reveals TNF-induced angiogenesis (2012)
  • Author(s): 尾上健太郎、山口類、井元清哉、玉田嘉紀、荒木啓充、Cristin Print、宮野悟
  • Organizer: The 23rd International Conference on Genome Informatics (GIW2012)
  • Place of Presentation: 台湾、台南市