In Silico Search for Drug Target Pathways by Gene Networks

• Project/Area Number: 18300097
• 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 The University of Tokyo, 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) ; NAGASAKI Masao 東京大学, 医科学研究所, 助教 (90396862) ; HISHIKI Teruyoshi 東邦大学, 理学部, 准教授 (30324271) ; YAMAGUCHI Rui 東京大学, 医科学研究所, 講師 (90380675) ; YOSHIDA Ryo 情報・システム研究機構, 統計数理研究所, 助教 (70401263) ; 土井 敦 東京大学, 医科学研究所, 特任助手
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥17,700,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥3,000,000); Fiscal Year 2008: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000); Fiscal Year 2007: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000); Fiscal Year 2006: ¥4,700,000 (Direct Cost: ¥4,700,000)
• Keywords: 遺伝子ネットワーク / システム生物学 / シミュレーション / 遺伝子発現マイクロアレイデータ / 創薬ターゲット遺伝子 / Fenofibrate / Gefitinib / 漢方薬 / マイクロアレイ / タンパク質相互作用 / 自己分泌パスウェイ

Research Abstract

遺伝子ノックダウンや薬剤応答などに基づいた遺伝子発現データから大規模遺伝子ネットワークを推定する方法と統計的解析とシミュレーションによる遺伝子ネットワークの解析方法を用いて, 遺伝子ネットワークに基づく, 創薬ターゲットパスウェイを探索するためのバイオインフォマティクス技術を開発した.この技術を使って, 薬剤Fenofibrate, Gefitinib 並びに漢方薬が影響を与えるパスウェイの解析を実現した.

Research Products

• [Journal Article] Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks (2009)
  • Author(s): Tamada, Y., Araki, H., Imoto, S., Nagasaki, M., Doi, A., Nakanishi, Y., Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D., Humphreys, S., Print, C., Charnock-Jones, D.S., Tashiro, K., Kuhara, S., Miyano, S.
  • Journal Title: Pacific Symposium on Biocomputing 14 Pages: 251-263
  • Peer Reviewed
• [Journal Article] Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine (2009)
  • Author(s): Watanabe-Fukuda, Y., Yamamoto, M., Miura, N., Fukutake, M., Ishige, A., Yamaguchi, R., Nagasaki, M., Saito, A., Imoto, S., Miyano, S., Takeda, J., Watanabe, K.
  • Journal Title: J.Gastroenterology 44(5) Pages: 380-389
  • NAID: 10025174631
  • Peer Reviewed
• [Journal Article] Unraveling dynamic activities of autocrine pathways that control drug-esponse transcriptome networks (2009)
  • Author(s): Tamada, Y., Araki, H., Imoto, S., Nagasaki, M., Doi, A., Nakanishi, Y. Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D., Humphreys, S., Print, C., Charnock-Jones, D. S., Tashiro, K., Kuhara, S., Miyano, S.
  • Journal Title: Pacific Symposium on Biocomputing 14 Pages: 251-263
  • Peer Reviewed
• [Journal Article] Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine (2009)
  • Author(s): Watanabe, Y., Yamamoto, M., Miura, N., Fukutake, M., Ishige, A., Yamaguchi, R., Nagasaki, M., Saito, A., Imoto, S., Miyano, S., Takeda, J., Watanabe, K.
  • Journal Title: J. Gastroenterology (印刷中)
  • NAID: 10025174631
  • Peer Reviewed
• [Journal Article] Gene-L' EXPO : a tool to extract knowledge from transcriptomes and find' literature-sparse' relationships between genes and tissues (2008)
  • Author(s): Hishiki, T., Tamada, I., Okubo, K.
  • Journal Title: Proc. AMIA Annual Symposium 2008 Pages: 313-317
  • Peer Reviewed
• [Journal Article] Predicting differences in gene regulatory systems by state space models (2008)
  • Author(s): Yamaguchi, R., Imoto, S., Yamauchi, M., Nagasaki, M., Yoshida, R., Shimamura, T., Hatanaka, Y., Ueno, K., Higuchi, T., Gotoh, N., Miyano, S.
  • Journal Title: Genome Informatics 21 Pages: 101-113
  • NAID: 130003997534
  • Peer Reviewed
• [Journal Article] Gene-L'EXPO: a Tool to Extract Knowledge From Transcriptomes and Find 'Literature-Sparse' Relationships Between Genes and Tissues (2008)
  • Author(s): Hishiki, T., Tamada, I., Okubo, K.
  • Journal Title: Proc. AMIA Annual Symposium 2008 Pages: 313-317
  • Peer Reviewed
• [Journal Article] Understanding endothelial cell apoptosis : What can the transcriptome glycome and proteome reveal (2007)
  • Author(s): Affara, M., Dunmore, B., Savoie, C.J., Imoto, S., Tamada, Y., Araki, H., Charnock-Jones, D.S., Miyano, S., Print, C.
  • Journal Title: Philosophical Transactions of Royal Society 362(1484) Pages: 1469-1487
  • Peer Reviewed
• [Journal Article] Statistical absolute evaluation of gene ontology terms with gene expression data (2007)
  • Author(s): Gupta, P.K., Yoshida, R., Imoto, S., Yamaguchi, R., Miyano, S.
  • Journal Title: Lecture Notes in Bioinformatics 4463 Pages: 146-157
  • Peer Reviewed
• [Journal Article] Analysis of gene networks for drug target discovery and validation (2007)
  • Author(s): Imoto, S., Tamada, Y., Savoie, C.J., Miyano, S.
  • Journal Title: Methods in Molecular Biology 360 Pages: 33-56
  • Peer Reviewed
• [Journal Article] Identification of activated transcription factors from microarray gene expression data of Kampo-medicine treated mice (2007)
  • Author(s): Yamaguchi, R., Yamamoto, M., Imoto, S., Nagasaki, M., Yoshida, R., Tsujii, K., Ishiga, A., Asou, H., Watanabe, K., Miyano, S.
  • Journal Title: Genome Informatics 18 Pages: 119-129
  • NAID: 130003812136
  • Peer Reviewed
• [Journal Article] Identification of activated transcription factors from microarray gene expression data of Kampo-medicine treated mice (2007)
  • Author(s): Yamaguchi, R., Yamamoto, M., Imoto, S., Nagasaki, M. Ybshida, R., Tsujii, K., Ishiga, A., Asou, H., Watanabe, K., Miano, S.
  • Journal Title: Genome Informatics 18 Pages: 119-129
  • NAID: 130003812136
  • Peer Reviewed
• [Journal Article] Understanding endothelial cell apoptosis:What can the transcriptome glycome and proteome reveal? (2007)
  • Author(s): Affara, M., Dunmore, B., Savoie, CJ., Imoto, S., Tamada, Y., Araki, H., Charnock-Jones, D.S., Miano, S., Print, C.
  • Journal Title: Philosophical Transactions of Royal Society B 362(1484) Pages: 1469-1487
  • Peer Reviewed
• [Journal Article] Estimating gene networks from gene expression data utilizing biological information (2006)
  • Author(s): Tamada, Y., Imoto, S., Miyano, S.
  • Journal Title: Proceedings of The Institute of Statistical Mathematics 54(2) Pages: 333-356
  • Peer Reviewed
• [Journal Article] Utilizing heterogeneous genomic data to estimate gene networks (2006)
  • Author(s): Tamada, Y., Imoto, S., Miyano, S.
  • Journal Title: Proceedings of The Institute of Statistical Mathematics 54・2 Pages: 315-332
  • NAID: 120006019063
• [Presentation] Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks, The 14^<th> Pacific Symposium on Biocomputing (2009)
  • Author(s): 宮野悟
  • Organizer: Fairmont Orchid
  • Place of Presentation: Big Island of Hawaii, USA
  • Year and Date: 2009-01-06
• [Presentation] Predicting differences in gene regulatory systems by state space models, The 19^<th> International Conference on Genome Informatics (2008)
  • Author(s): 宮野悟
  • Organizer: Coast
  • Place of Presentation: Australia
  • Year and Date: 2008-12-02
• [Presentation] Gene-L' EXPO : a Tool to Extract Knowledge From Transcriptomes and Find ' Literature-Sparse' Relationships Between Genes and Tissues (2008)
  • Author(s): 日紫喜光良
  • Organizer: AMIA Annual Symposium
  • Place of Presentation: Washington D.C., USA
  • Year and Date: 2008-11-10
• [Presentation] Gene-L'EXPO: a Tool to Extract Knowledge From Transcriptomes and Find 'Literature-Sparse' Relationships Between Genes and Tissues (2008)
  • Author(s): Hishiki, T.
  • Organizer: AMIA Annual Symposium 2008
  • Place of Presentation: Washington D. C., USA
  • Year and Date: 2008-11-10
• [Presentation] Computational Systems Biology 2007 (2007)
  • Author(s): 宮野悟
  • Organizer: INDY Bioinformatics Conference
  • Place of Presentation: Indiana University Medical School, Indianapolis, USA.
  • Year and Date: 2007-06-01
• [Presentation] Computational Systems Biology (2007)
  • Author(s): Miyano, S.
  • Organizer: 2007INDY Bioinformatics Conference
  • Place of Presentation: Indiana University Medical School,Indianapolis,USA
  • Year and Date: 2007-06-01
• [Presentation] Computational Challenges for Top-Down Modeling and Simulation of Biological Pathways (2006)
  • Author(s): 宮野悟
  • Organizer: The 3^<rd> International E. Coli Alliance Conference on Systems Biology(International Convention Center Jeju)
  • Place of Presentation: Republic of Korea
  • Year and Date: 2006-11-01
• [Presentation] Computational Systems Biology and Its Applications to Drug Target Gene Discovery (2006)
  • Author(s): 宮野悟
  • Organizer: INTERNATIONAL CONGRESS OF IMMUNOGENOMICS AND IMMUNOMICS 2006(Budapest Congress & World Trade Center, Budapest)
  • Place of Presentation: Hungary
  • Year and Date: 2006-10-11
• [Presentation] Gene Networks for Drug Target Pathway Discover (2006)
  • Author(s): 宮野悟
  • Organizer: The First Toxicomics Forum
  • Place of Presentation: 名古屋国際会議場 センチュリーホール
  • Year and Date: 2006-07-05
• [Remarks] MetaGeneProfiler による解析サービスサイト
  • URL: http://metagp.ism.ac.jp/