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Establishment of proteomics analysis methods using RNA-seq in the personal genomic era

Research Project

Project/Area Number 16K00416
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research Institution大学共同利用機関法人情報・システム研究機構(機構本部施設等)

Principal Investigator

Kawano Shin  大学共同利用機関法人情報・システム研究機構(機構本部施設等), データサイエンス共同利用基盤施設, 客員准教授 (40470075)

Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2018: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywordsプロテオーム / パーソナルゲノム / プロテオゲノミクス / バイオマーカー / ゲノム
Outline of Final Research Achievements

In this research project, I examined effective analysis methods of proteome data including mutations, such as human personal proteome and cancer proteome obtained using a mass spectrometer. By analyzing proteome data using a protein sequence database considering mutations, which was created by detecting mutations from DNA / RNA sequences using a next-generation sequencer, it became possible to detect peptides containing sample-specific mutations which has not been possible to detect using conventional methods.

Academic Significance and Societal Importance of the Research Achievements

さまざまなゲノムの変異が病気に関係しているが、実際に生体内で作用して機能を担っているのは発現しているタンパク質である。変異を含むタンパク質を検出可能にすることは、病気に関係するバイオマーカーの発見や創薬につながる。今後、次世代シーケンサーならびに質量分析計の測定精度がますます向上していくと予想され、“個人”のマルチオミクス情報を組み合わせた解析は、precision medicineを実現する上で必要不可欠なものになると期待される。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (29 results)

All 2018 2017 2016 Other

All Int'l Joint Research (8 results) Journal Article (4 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 4 results,  Open Access: 4 results,  Acknowledgement Compliant: 1 results) Presentation (16 results) (of which Int'l Joint Research: 5 results,  Invited: 4 results) Remarks (1 results)

  • [Int'l Joint Research] European Bioinformatics Institute(英国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] University of California San Diego/Institute for Systems Biology/University of Washington(米国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Beijing Institute of Life Omics(中国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Academia Sinica(その他の国・地域)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] European Bioinformatics Institute(United Kingdom)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] Institute for Systems Biology(米国)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] Academia Sinica(Taiwan)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] European Bioinformatics Institute(United Kingdom)

    • Related Report
      2016 Research-status Report
  • [Journal Article] The jPOST environment: an integrated proteomics data repository and database2018

    • Author(s)
      Moriya Yuki、Kawano Shin、Okuda Shujiro、Watanabe Yu、Matsumoto Masaki、Takami Tomoyo、Kobayashi Daiki、Yamanouchi Yoshinori、Araki Norie、Yoshizawa Akiyasu C、Tabata Tsuyoshi、Iwasaki Mio、Sugiyama Naoyuki、Tanaka Satoshi、Goto Susumu、Ishihama Yasushi
    • Journal Title

      Nucleic Acids Research

      Volume: 47 Issue: D1 Pages: 1218-1224

    • DOI

      10.1093/nar/gky899

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Proteomics Standards Initiative: Fifteen Years of Progress and Future Work2017

    • Author(s)
      Deutsch Eric W.、Orchard Sandra、Binz Pierre-Alain、Bittremieux Wout、Eisenacher Martin、Hermjakob Henning、Kawano Shin、Lam Henry、Mayer Gerhard、Menschaert Gerben、Perez-Riverol Yasset、Salek Reza M.、Tabb David L.、Tenzer Stefan、Vizca?no Juan Antonio、Walzer Mathias、Jones Andrew R.
    • Journal Title

      Journal of Proteome Research

      Volume: 16 Issue: 12 Pages: 4288-4298

    • DOI

      10.1021/acs.jproteome.7b00370

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] jPOSTrepo: an international standard data repository for proteomes.2017

    • Author(s)
      Okuda S, Watanabe Y, Moriya Y, Kawano S, Yamamoto T, Matsumoto M, Takami T, Kobayashi D, Araki N, Yoshizawa AC, Tabata T, Sugiyama N, Goto S, Ishihama Y.
    • Journal Title

      Nucleic Acids Res.

      Volume: 45 Issue: D1 Pages: D1107-D1111

    • DOI

      10.1093/nar/gkw1080

    • NAID

      120006353864

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] The ProteomeXchange Consortium in 2017: supporting the cultural change in proteomics public data deposition.2017

    • Author(s)
      Deutsch, E. W., Csordas, A., Sun, Z., Jarnuczak, A., Perez-Riverol, Y., Ternent, T., Campbell, D. S., Bernal-Llinares, M., Okuda, S., Kawano, S., Moritz, R. L., Carver, J. J., Wang, M., Ishihama, Y., Bandeira, N., Hermjakob, H., Vizcaíno, J. A.
    • Journal Title

      Nucleic Acids Res.

      Volume: 45 Issue: D1 Pages: D1100-D1106

    • DOI

      10.1093/nar/gkw936

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] jPOST: 質量分析生データを最大限に活用するためのメタデータキュレーション2018

    • Author(s)
      小林大樹、荒木令江、奥田修二郎、渡辺由、守屋勇樹、河野信、山本格、松本雅記、高見知代、吉沢明康、田畑剛、岩崎未央、杉山直幸、田中聡、五斗進、石濱泰
    • Organizer
      Mass Spectrometry and Proteomics 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] プロテオーム統合データベースの機能深化2018

    • Author(s)
      守屋勇樹、河野信、奥田修二郎、渡邉由、松本雅記、高見知代、小林大樹、山ノ内祥訓、荒木令江、吉沢明康、田畑剛、岩崎未央、杉山直幸、田中聡、五斗進、石濱泰
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] jPOSTプロジェクトが提供するプロテオミクスデータとその解析ツール2018

    • Author(s)
      五斗進、守屋勇樹、河野信、奥田修二郎、渡邉由、松本雅記、高見知代、小林大樹、山ノ内祥訓、荒木令江、吉沢明康、田畑剛、岩崎未央、杉山直幸、田中聡、石濱泰
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 機械学習に基づくペプチド由来イオンピークの新規検出手法2018

    • Author(s)
      守屋勇樹、田畑剛、岩崎未央、河野信、五斗進、石濱泰、瀧川一学、吉沢明康
    • Organizer
      第21回情報論的学習理論ワークショップ
    • Related Report
      2018 Annual Research Report
  • [Presentation] Controlling false discovery rate in accumulated public proteome dataset2017

    • Author(s)
      Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Yuki Moriya, Shin Kawano, Shujiro Okuda, Yu Watanabe, Tadashi Yamamoto, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Norie Araki, Naoyuki Sugiyama, Satoshi Tanaka, Susumu Goto, and Yasushi Ishihama
    • Organizer
      65th Conference on Mass Spectrometry and Allied Topics
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] プロテオームデータの標準化とデータベースの世界動向2017

    • Author(s)
      河野信
    • Organizer
      日本プロテオーム学会2017年大会
    • Related Report
      2017 Research-status Report
  • [Presentation] jPOST 再解析プロトコル:偽陽性と偽陰性の同時減少を目指す2017

    • Author(s)
      吉沢明康、田畑剛、守屋勇樹、河野信、奥田修二郎、渡辺由、山本格、松本雅記、高見知代、小林大樹、荒木令江、杉山直幸、田中聡、五斗進、石濱泰
    • Organizer
      日本プロテオーム学会2017年大会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] jPOST: プロテオーム統合データベースの開発2017

    • Author(s)
      守屋勇樹、河野信、奥田修二郎、渡辺由、山本格、松本雅記、高見知代、小林大樹、荒木令江、吉沢明康、田畑剛、杉山直幸、田中聡、五斗進、石濱泰
    • Organizer
      日本プロテオーム学会2017年大会
    • Related Report
      2017 Research-status Report
  • [Presentation] OmicsDI RDF2017

    • Author(s)
      Shin Kawano, Yasset Perez Riverol, Tobias Ternent, Yuki Moriya, Eric Deutsch, Michel Dumontier, Juan Antonio Vizcaino, Henning Hermjakob, and Susumu Goto
    • Organizer
      16th Human Proteome Organization World Congress
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Controlling false discovery rates on large-scale proteome datasets in jPOST2017

    • Author(s)
      Yasuhi Ishihama, Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Yuki Moriya, Shin Kawano, Shujiro Okuda, Yu Watanabe, Tadashi Yamamoto, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Norie Araki, Naoyuki Sugiyama, Satoshi Tanaka, and Susumu Goto
    • Organizer
      16th Human Proteome Organization World Congress
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 生命システムを俯瞰するための質量分析情報解析技術とデータベースの活用2016

    • Author(s)
      河野信
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川県・横浜市)
    • Year and Date
      2016-11-30
    • Related Report
      2016 Research-status Report
  • [Presentation] Implementation of flexible search for proteomics metadata2016

    • Author(s)
      Shin Kawano, Yuki Moriya, Tobias Ternent, Juan Antonio Vizcaino, Eric Deutsch
    • Organizer
      15th Human Proteome Organization World Congress
    • Place of Presentation
      Taipei International Convention Center(台湾・台北)
    • Year and Date
      2016-09-18
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] プロテオームインフォマティクス&システムズバイオロジー研究への招待2016

    • Author(s)
      河野信、荒木令江
    • Organizer
      日本プロテオーム学会2016年大会
    • Place of Presentation
      北里大学(東京都・港区)
    • Year and Date
      2016-07-28
    • Related Report
      2016 Research-status Report
  • [Presentation] プロテオームデータベース jPOST の開発2016

    • Author(s)
      五斗進、奥田修二郎、渡邉由、守屋勇樹、河野信、山本格、松本雅記、高見知代、小林大樹、荒木令江、吉沢明康、田畑剛、杉山直幸、石濱泰
    • Organizer
      日本プロテオーム学会2016年大会
    • Place of Presentation
      北里大学(東京都・港区)
    • Year and Date
      2016-07-28
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] プロテオーム統合データベース jPOST:再解析プロトコルの開発2016

    • Author(s)
      吉沢明康、田畑剛、守屋勇樹、河野信、奥田修二郎、渡邉由、山本格、松本雅記、高見知世、小林大樹、荒木令江、杉山直幸、五斗進、石濱泰
    • Organizer
      日本プロテオーム学会2016年大会
    • Place of Presentation
      北里大学(東京都・港区)
    • Year and Date
      2016-07-28
    • Related Report
      2016 Research-status Report
  • [Presentation] 質量スペクトルはデータベース検索“グレーゾーン”を明瞭化するか2016

    • Author(s)
      吉沢明康、田畑剛、守屋勇樹、河野信、奥田修二郎、山本格、松本雅記、小林大樹、荒木令江、杉山直幸、五斗進、石濱泰
    • Organizer
      日本質量分析学会 第64回質量分析総合討論会
    • Place of Presentation
      ホテル阪急エキスポパーク(大阪府・吹田市)
    • Year and Date
      2016-05-18
    • Related Report
      2016 Research-status Report
  • [Remarks] jPOSTdb

    • URL

      https://globe.jpostdb.org/

    • Related Report
      2018 Annual Research Report

URL: 

Published: 2016-04-21   Modified: 2022-02-22  

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