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Improved identification of drug targets by data warehousing and simulations of signal transduction pathways

Research Project

Project/Area Number 17K07268
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field System genome science
Research InstitutionNational Institutes of Biomedical Innovation, Health and Nutrition

Principal Investigator

Mizuguchi Kenji  国立研究開発法人医薬基盤・健康・栄養研究所, 医薬基盤研究所 AI健康・医薬研究センター, センター長 (50450896)

Co-Investigator(Kenkyū-buntansha) 伊藤 眞里  国立研究開発法人医薬基盤・健康・栄養研究所, 医薬基盤研究所 AI健康・医薬研究センター, 上席研究員 (50728102)
Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2019: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2018: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2017: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywordsトランスオミックス解析 / 代謝物情報 / 統合データベース / KEGGパスウェイ / エンリッチメント解析 / タンパク質間相互作用 / バイオインフォマティクス / 創薬ターゲット
Outline of Final Research Achievements

In drug discovery and disease biology, the rapid proliferation of high-throughput ‘omics’ data has necessitated a need for tools that allow the researchers to combine and analyze different types of biological data. TargetMine is an integrative data analysis platform for target prioritization and broad-based biological knowledge discovery. In this study, we added new functions to TargetMine, treating new biological data types and enhanced visual and analytical features. First, to facilitate a more effective metabolomics analysis with TargetMine, we integrated the compound database KEGG COMPOUND, as well as KEGG reactions. As a result, given a list of compounds, the users can retrieve the enzymatic reactions involving these metabolites and map them to the corresponding pathways. Second, we evaluated all protein-protein interactions (PPIs) in TargetMine using our own in silico prediction method, and individual PPIs were tagged with scores of new attributes of reliability.

Academic Significance and Societal Importance of the Research Achievements

創薬研究において、開発が容易な創薬ターゲットに作用する薬剤はすでに研究開発し尽くされ、現在残っているのは高難易度の創薬ターゲットのみであること、また難病などにおいて、まだ真の標的が見いだされていないことなどから、「創薬ターゲットの枯渇」が深刻化している。この課題に対応するため、ヒトゲノム等の生体分子のデータと臨床データや医学、生物学的データ、医薬品関連のデータなどとの統合的な解析により、疾患病態の解明や真の創薬ターゲットの発見につなげることが求められている。本研究成果は、この統合的な解析のツールを提供し、真の創薬ターゲットを導き出すための支援につながるものである

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (43 results)

All 2020 2019 2018 2017

All Journal Article (16 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 10 results,  Open Access: 10 results) Presentation (27 results) (of which Int'l Joint Research: 3 results,  Invited: 24 results)

  • [Journal Article] The TargetMine data warehouse: enhancement and updates2019

    • Author(s)
      Chen Y.A., Tripathi L.P., Fujiwara T., Kameyama T., Ito M., Mizuguchi K.
    • Journal Title

      Frontiers in Genetics-Bioinformatics and Computational Biology

      Volume: 10 Pages: 934-934

    • DOI

      10.3389/fgene.2019.00934

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Data Warehousing with TargetMine for Omics Data Analysis2019

    • Author(s)
      Chen Y.A., Tripathi L.P., Mizuguchi K.
    • Journal Title

      Methods in Molecular Biology

      Volume: 1986 Pages: 35-64

    • DOI

      10.1007/978-1-4939-9442-7_3

    • ISBN
      9781493994410, 9781493994427
    • Related Report
      2019 Annual Research Report
  • [Journal Article] Integrative Analysis of Multi-Omics Data2019

    • Author(s)
      Tripathi L.P., Esaki T., Itoh M., Chen Y.A, Mizuguchi K.
    • Journal Title

      Encyclopedia of Bioinformatics and Computational Biology

      Volume: 3 Pages: 194-199

    • DOI

      10.1016/b978-0-12-809633-8.20096-4

    • ISBN
      9780128114322
    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Assessing drug target suitability using Targetmine2019

    • Author(s)
      Chen Y.A., Yogo E., Kurihara N., Ohno T., Higuchi C., Rokushima M., Mizuguchi K.
    • Journal Title

      F1000Research

      Volume: 8 Pages: 233-233

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Data Warehousing with TargetMine for Omics Data Analysis2019

    • Author(s)
      Chen Y.A., Tripathi L.P., Mizuguchi K.
    • Journal Title

      Methods Molecular Biology 1986(Microarray Bioinformatics)

      Volume: 印刷中

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] TargetMineによる標的予測2018

    • Author(s)
      夏目やよい, 相崎健一, 北嶋聡, 陳怡安, 水口賢司, 菅野純
    • Journal Title

      The Journal of Toxicological Sciences

      Volume: 43

    • NAID

      130007432170

    • Related Report
      2018 Research-status Report
    • Open Access
  • [Journal Article] 創薬における計算機の果たす役割 -プレシジョンメディシンに向けて-2018

    • Author(s)
      長尾知生子, 夏目やよい, 水口賢司
    • Journal Title

      Precision Medicine

      Volume: 1(1) Pages: 28-31

    • Related Report
      2018 Research-status Report
  • [Journal Article] バイオメディカル・基礎から臨床への開発プロセス(1)~人工知能を用いる創薬テーマ創出2018

    • Author(s)
      伊藤眞里
    • Journal Title

      医薬ジャーナル

      Volume: 54(9) Pages: 2029-2032

    • Related Report
      2018 Research-status Report
  • [Journal Article] Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism2018

    • Author(s)
      Ahmad Shandar、Prathipati Philip、Tripathi Lokesh P、Chen Yi-An、Arya Ajay、Murakami Yoichi、Mizuguchi Kenji
    • Journal Title

      Nucleic Acids Research

      Volume: 46 Issue: 1 Pages: 54-70

    • DOI

      10.1093/nar/gkx1166

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Double deletion of tetraspanins CD9 and CD81 in mice leads to a syndrome resembling accelerated aging2018

    • Author(s)
      Jin Y, Takeda Y, Kondo Y, Tripathi LP, Kang S, Takeshita H, Kuhara H, Maeda Y, Higashiguchi M, Miyake K, Morimura O、Koba T、Hayama Y、Koyama S、Nakanishi K、Iwasaki T、Tetsumoto Si、Tsujino K、Kuroyama M、Iwahori K、Hirata H、Takimoto Ti、Suzuki M、Nagatomo I、Sugimoto K、Fujii Y、Kida H、et al.
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 5145-5145

    • DOI

      10.1038/s41598-018-23338-x

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Network-based analysis for biological discovery2018

    • Author(s)
      Tripathi Lokesh P.、Murakami Yoichi、Chen Yi-An.、Mizuguchi Kenji
    • Journal Title

      Encyclopedia of Bioinformatics and Computational Biology

      Volume: -

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Integrative analysis of Multi-omics data2018

    • Author(s)
      Tripathi Lokesh P.、Esaki Tsuyoshi、Ito Mari、Chen Yi-An.、Mizuguchi Kenji
    • Journal Title

      Encyclopedia of Bioinformatics and Computational Biology

      Volume: -

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] PSOPIA: Toward more reliable protein-protein interaction prediction from sequence information2017

    • Author(s)
      Murakami Yoichi、Mizuguchi Kenji
    • Journal Title

      IEEE Conferences

      Volume: - Pages: 255-261

    • DOI

      10.1109/iciibms.2017.8279749

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Making protein-protein interaction prediction more reliable with a large-scale dataset at the proteome level2017

    • Author(s)
      Murakami Yoichi、Mizuguchi Kenji
    • Journal Title

      Journal of Bioinformatics and Neuroscience

      Volume: 3 Pages: 91-98

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] 公共データベースの統合からAIによるデータマイニングに向けて2017

    • Author(s)
      伊藤 眞里、長尾 知生子、夏目 やよい、水口 賢司
    • Journal Title

      CICSJ Bulletin

      Volume: 35 Issue: 3 Pages: 210

    • DOI

      10.11546/cicsj.35.210

    • NAID

      130006792845

    • ISSN
      0913-3747, 1347-2283
    • Related Report
      2017 Research-status Report
    • Open Access
  • [Journal Article] Database Development and Computational Modelling in Early-Stage Drug Discovery2017

    • Author(s)
      水口 賢司
    • Journal Title

      TRENDS IN THE SCIENCES

      Volume: 22 Issue: 7 Pages: 7_62-7_65

    • DOI

      10.5363/tits.22.7_62

    • NAID

      130006882503

    • ISSN
      1342-3363, 1884-7080
    • Related Report
      2017 Research-status Report
    • Open Access
  • [Presentation] 疾患・創薬研究におけるデータベースとAI活用2020

    • Author(s)
      水口賢司
    • Organizer
      日本臨床試験学会 第11回学術集会総会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 創薬研究へのAI活用2020

    • Author(s)
      水口賢司
    • Organizer
      ILSI Japan先端技術シンポジウム
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] AI創薬の基礎としてのデータ統合とモデリング2019

    • Author(s)
      水口賢司
    • Organizer
      第6回NPO法人京都コモンズ 会員セミナー
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] AI創薬基盤としてのデータ統合とデータベース開発2019

    • Author(s)
      水口賢司
    • Organizer
      ゲノム創薬・創発フォー ラム第1回シンポジウム
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Data integration as a basis for artificial intelligence in drug discovery2019

    • Author(s)
      水口賢司
    • Organizer
      第14回生命医科学研究所ネットワーク国際シンポジウム
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Data integration and computational systems approaches to drug discovery2019

    • Author(s)
      水口賢司
    • Organizer
      6th International Symposium on Diffraction Structural Biology (ISDSB2019)
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Artificial intelligence-based drug discovery: challenges and applications to target identification and pharmacokinetic modelling2019

    • Author(s)
      水口賢司
    • Organizer
      第4回トランスオミクスシンポジウム
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] AI開発基盤としてのデータ統合:薬物動態モデリングとターゲット探索2019

    • Author(s)
      水口賢司
    • Organizer
      第1回日本メディカルAI学会学術集会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] データ統合と人工知能技術による新薬創出の加速2019

    • Author(s)
      水口賢司
    • Organizer
      彩都産学官連携フォーラム 2019
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 計算生物学と創薬のためのデータ統合2019

    • Author(s)
      水口賢司
    • Organizer
      シンポジウム「理論生物物理学の現在と未来」
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] インフォマティクスの活用による新薬創出の加速を目指して2019

    • Author(s)
      水口賢司
    • Organizer
      第5回インターフェックス大阪
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] データ統合と計算システム生物学による創薬2019

    • Author(s)
      水口賢司
    • Organizer
      バイオインタラクション研究会 第4回ワークショップ
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Adding trans-omics analysis features to TargetMine2018

    • Author(s)
      Kameyama T., Chen Y.A., Nojima Y., Fujiwara T., Esaki T., Tripathi L., Ito M., Mizuguchi K.
    • Organizer
      CBI学会2018年 大会
    • Related Report
      2018 Research-status Report
  • [Presentation] 創薬・健康・栄 養研究を支援する支援するNIBIOHNのデータベース2018

    • Author(s)
      水口賢司, 坂手龍一, 五十嵐芳暢, 陳怡安, 樋口千洋, 長尾知生子, 深川明子
    • Organizer
      第41回日本分子生物学会年会(特別企画バイオデータベースコーナー)
    • Related Report
      2018 Research-status Report
  • [Presentation] タンパク質インフォマティクスのためのデータ統合2018

    • Author(s)
      水口賢司
    • Organizer
      第18回日本蛋白質科学会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 創薬におけるAI利活用2018

    • Author(s)
      水口賢司
    • Organizer
      CBI学会(情報計算化学生物学会)2018年大会(プレナリー講演)
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Data integration and computational systems approaches towards rational drug discovery2018

    • Author(s)
      水口賢司
    • Organizer
      InCoB 2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Data integration as a basis for computational modelling for rational drug discovery2018

    • Author(s)
      Mizuguchi K.
    • Organizer
      The 18th KIAS Conference on Protein Structure and Function
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Data integration and computational systems approaches to target discovery and pharmacokinetic modelling2018

    • Author(s)
      水口賢司
    • Organizer
      日英セミナー Big Data and AI in Drug Discovery: Resources and Developments
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Data integration and computational modelling for drug discovery2018

    • Author(s)
      水口賢司
    • Organizer
      第6回ITbM国際シンポジウム
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 創薬・疾患研究のためのデータ統合の実際2018

    • Author(s)
      水口賢司
    • Organizer
      トーゴーの日シンポジウム2018
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] AIと創薬2018

    • Author(s)
      伊藤眞里
    • Organizer
      NPO法人J-Win Next Stage 『第四次産業革命研究会』
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] タンパク質立体構造の比較とデータベース2017

    • Author(s)
      水口賢司
    • Organizer
      第386回CBI学会講演会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 多階層データの統合モデリングによる薬物動態予測 システムの構築2017

    • Author(s)
      水口賢司
    • Organizer
      CBI学会2017年大会フォーカストセッション
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Data integration and statistical/ab initio modeling towards rational drug discovery2017

    • Author(s)
      水口賢司
    • Organizer
      The 55th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 創薬・健康・栄養 研究を支援するNIBIOHNのデータベース2017

    • Author(s)
      水口賢司,坂手龍一,深川明子,五十嵐芳暢,陳怡安,樋口千洋,長尾知生子
    • Organizer
      2017年度生命科学系学会合同年次大会 (ConBio2017)
    • Related Report
      2017 Research-status Report
  • [Presentation] データ統合と多階層モデリングによる創薬の効率化2017

    • Author(s)
      水口賢司
    • Organizer
      徳島大学研究クラスター 統合的がん創薬研究クラスター 特別セミナー
    • Related Report
      2017 Research-status Report
    • Invited

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Published: 2017-04-28   Modified: 2021-02-19  

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