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Deciphering positive and negative selection in thymocyte from information theoretic approach

Research Project

Project/Area Number 18H02431
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43060:System genome science-related
Research InstitutionKyushu University

Principal Investigator

Uda Shinsuke  九州大学, 生体防御医学研究所, 准教授 (20599609)

Co-Investigator(Kenkyū-buntansha) 幡野 敦  新潟大学, 医歯学系, 助教 (30755533)
比嘉 綱己  九州大学, 生体防御医学研究所, 学術研究員 (60826238)
Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Fiscal Year 2020: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2019: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2018: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Keywords情報理論 / システム生物学 / 胸腺T細胞 / シグナル伝達 / 生命科学 / 情報 / 正負の選択
Outline of Final Research Achievements

We measured and acquired the data set to analyze signal transduction in thymocyte at single cell level by information theory. The data set is composed of 6000 cells per time point, because the analysis base on information theory requires a large sample size. The result suggests that dynamics of information transmission of S6 is specific compared to another signaling molecules. We developed the quantitative visualization method of communication channel of signaling molecules and applied to the data set. We found that the communication channel of S6 was different from another signaling molecules.

Academic Significance and Societal Importance of the Research Achievements

胸腺T細胞の正負の選択におけるシグナル伝達の情報理論的解析はなく,生物学的にも情報伝達の全貌は未解明のままである.本研究により,情報量という定量的尺度を導入した解析によって,新たな知見が得られる可能性は高い.特に,通信路の観点からのシグナル伝達系の解析はほとんどなく,通信路の違いの可視化は本研究の実験系だけでなく,一般の系にも適用可能で広く応用できる可能性がある.

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (7 results)

All 2020 2019 2018

All Journal Article (5 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 5 results,  Open Access: 5 results) Presentation (2 results) (of which Int'l Joint Research: 1 results)

  • [Journal Article] Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity2020

    • Author(s)
      Kokaji Toshiya、Hatano Atsushi、Ito Yuki、et al.
    • Journal Title

      Science Signaling

      Volume: 13 Issue: 660 Pages: 1236-1236

    • DOI

      10.1126/scisignal.aaz1236

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise2020

    • Author(s)
      Wada Takumi、Hironaka Ken-ichi、Wataya Mitsutaka、Fujii Masashi、Eto Miki、Uda Shinsuke、Hoshino Daisuke、Kunida Katsuyuki、Inoue Haruki、Kubota Hiroyuki、Takizawa Tsuguto、Karasawa Yasuaki、Nakatomi Hirofumi、Saito Nobuhito、Hamaguchi Hiroki、Furuichi Yasuro、Manabe Yasuko、Fujii Nobuharu L.、Kuroda Shinya
    • Journal Title

      Cell Reports

      Volume: 32 Issue: 9 Pages: 108051-108051

    • DOI

      10.1016/j.celrep.2020.108051

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Application of information theory in systems biology2020

    • Author(s)
      Shinsuke Uda
    • Journal Title

      Biophysical Review

      Volume: - Issue: 2 Pages: 377-384

    • DOI

      10.1007/s12551-020-00665-w

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Trans-omics impact of thymoproteasome in cortical thymic epithelial cells.2019

    • Author(s)
      Ohigashi I, Tanaka Y, Kondo K, Fujimori S, Kondo H, Palin A, Hoffmann V, Kozai M, Matsushita Y, Uda S, Motosugi R, Hamazaki J, Kubota H, Murata S, Tanaka K, Katagiri T, Kosako H, Takahama Y
    • Journal Title

      Cell Reports

      Volume: 29 Issue: 9 Pages: 2901-2916

    • DOI

      10.1016/j.celrep.2019.10.079

    • NAID

      120006894616

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data2018

    • Author(s)
      Kawata Kentaro、Yugi Katsuyuki、Hatano Atsushi、Kokaji Toshiya、Tomizawa Yoko、Fujii Masashi、Uda Shinsuke、Kubota Hiroyuki、Matsumoto Masaki、Nakayama Keiichi I.、Kuroda Shinya
    • Journal Title

      Genes to Cells

      Volume: 24 Issue: 1 Pages: 82-93

    • DOI

      10.1111/gtc.12655

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Comparison of hepatic responses to glucose perturbation between normal and obese mice using edge ontology2020

    • Author(s)
      Yuki Ito, Shinsuke Uda, Toshiya Kokaji, Akiyoshi Hirayama, Tomoyoshi Soga, Yutaka Suzuki, Shinya Kuroda and Hiroyuki Kubota
    • Organizer
      Fusion of Mathematics and Biology
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Comparison of hepatic metabolome and transcriptome responses to oral glucose tolerance test between normal and obese mice by information theoretic approach2019

    • Author(s)
      Yuki Ito, Shinsuke Uda, Toshiya Kokaji, Akiyoshi Hirayama, Tomoyoshi Soga, Yutaka Suzuki, Shinya Kuroda and Hiroyuki Kubota
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report

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Published: 2018-04-23   Modified: 2022-01-27  

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