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Study of Information analysis and modelinig

Planned Research

Project AreaPreventive medicine through inflammation cellular sociology
Project/Area Number 17H06399
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionNational Institute of Genetics

Principal Investigator

IKEO KAZUHO  国立遺伝学研究所, ゲノム・進化研究系, 准教授 (20249949)

Co-Investigator(Kenkyū-buntansha) 渡邉 日出海  北海道大学, 情報科学研究院, 教授 (30322754)
太田 聡史  国立研究開発法人理化学研究所, 光量子工学研究センター, 専任研究員 (30391890)
小倉 淳  長浜バイオ大学, バイオサイエンス学部, 教授 (60465929)
Project Period (FY) 2017-06-30 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥137,020,000 (Direct Cost: ¥105,400,000、Indirect Cost: ¥31,620,000)
Fiscal Year 2021: ¥26,260,000 (Direct Cost: ¥20,200,000、Indirect Cost: ¥6,060,000)
Fiscal Year 2020: ¥26,260,000 (Direct Cost: ¥20,200,000、Indirect Cost: ¥6,060,000)
Fiscal Year 2019: ¥26,260,000 (Direct Cost: ¥20,200,000、Indirect Cost: ¥6,060,000)
Fiscal Year 2018: ¥26,260,000 (Direct Cost: ¥20,200,000、Indirect Cost: ¥6,060,000)
Fiscal Year 2017: ¥31,980,000 (Direct Cost: ¥24,600,000、Indirect Cost: ¥7,380,000)
Keywords単一細胞トランスクリプトーム / 炎症細胞の遷移 / NGSデータ解析 / 細胞系譜再構築 / データベース / マーカー遺伝子探索 / 体細胞変異 / 炎症モデル構築 / 状態遷移マーカー遺伝子探索 / ゲノム / 細胞社会モデル / 単一細胞トランスクリプトーム解析 / 細胞系譜 / 細胞マーカー遺伝子 / クラスタリング
Outline of Final Research Achievements

We constructed a single-cell data portal, analyzed the data collected from the research groups in the area, and released all the data in a form that can be downloaded and displayed.
It was shown that a cell lineage consistent with known knowledge can be estimated using a somatic mutation pattern at the 1-cell level for the construction of a dynamic model of a cell population. We also reviewed conventional machine learning methods and succeeded in developing a mathematical method for extracting useful information on gene interactions and co-expressions from less cell expression data. Using a machine learning model, we made it possible to extract disease-related genes from the enrichment analysis of the APA disrupted gene list.

Academic Significance and Societal Importance of the Research Achievements

今後ますます増加していくシングルセルデータの解析の発展に大きく貢献することが期待される解析フローを構築した。これは、今後、医学領域に加え、基礎生物学領域での利用も期待される。また、少数細胞のデータから既知の細胞種を選別することばかりでなく、新規の細胞種の定義を定量的に行うことが可能となった。細胞系譜再構築手法を加えて、シングルセルレベルのデータを大規模かつ効率的に解析する手法は今後、様々な単一細胞研究に貢献することが期待される。炎症細胞社会データベースとして公開した領域全体のデータは、様々な疾患に関わる炎症の分子レベルでの理解の助けとなることが期待される。

Report

(6 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (10 results)

All 2022 2021 2020 2019 2018 Other

All Journal Article (8 results) (of which Open Access: 8 results,  Peer Reviewed: 6 results) Presentation (1 results) Remarks (1 results)

  • [Journal Article] Real-Time Course: Reconstruction of cellular diversity and lineage trajectory based on somatic mutational patterns detected from low-pass single-cell transcriptome data2022

    • Author(s)
      1.Satoshi Oota*, Kuniya Abe, Hideo Yokota, Kazuho Ikeo.
    • Journal Title

      Research Square

      Volume: なし Pages: 1-22

    • DOI

      10.21203/rs.3.rs-1558242/v1

    • Related Report
      2021 Annual Research Report
    • Open Access
  • [Journal Article] Collagen adhesion gene is associated with bloodstream infections caused by methicillin-resistant Staphylococcus aureus.2020

    • Author(s)
      Iwata Y, Satou K, Furuichi K, Yoneda I, Matsumura T, et al.
    • Journal Title

      Int J Infect Dis.

      Volume: 91 Pages: 22-31

    • DOI

      10.1016/j.ijid.2019.11.003

    • NAID

      120006842044

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The increased frequency of methicillin-resistant Staphylococcus aureus with low MIC of beta-lactam antibiotics isolated from hospitalized patients2020

    • Author(s)
      Iwata Y、Sakai N、Yoneda I、Satou K、Furuichi K、Senda Y、Sakai-Takemori Y、Wada T、Fujita S、Ogura H、Sato K、Minami T、Yamaguchi K、Kitajima S、Toyama T、Yamamura Y、Miyagawa T、Hara A、Shimizu M、Sakai Y、Ikeo K、Shichino S、Ueha S、Nakajima T、Matsushima K、Wada T
    • Journal Title

      Journal of Infection and Chemotherapy

      Volume: 26 Issue: 6 Pages: 604-610

    • DOI

      10.1016/j.jiac.2020.01.016

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] DOCK11 and DENND2A play pivotal roles in the maintenance of hepatitis B virus in host cells.2020

    • Author(s)
      Hashimoto S, Shirasaki T, Yamashita T, Iwabuchi S, Suzuki Y, Takamura Y, Ukita Y, Deshimaru S, Okayama T, Ikeo K, Kuroki K, Kawaguchi K, Mizukoshi E, Matsushima K, Honda M, Kaneko S
    • Journal Title

      PLoS One

      Volume: 16(2) Issue: 2 Pages: e0246313-e0246313

    • DOI

      10.1371/journal.pone.0246313

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The reduction of miR146b-5p in monocytes and T cells could contribute to the immunopathogenesis of hepatitis C virus infection2019

    • Author(s)
      Kondo Yasuteru、Kogure Takayuki、Ninomiya Masashi、Fukuda Ryo、Monma Norikazu、Ikeo Kazuho、Tanaka Yasuhito
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 13393-13393

    • DOI

      10.1038/s41598-019-49706-9

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Specific features of fibrotic lung fibroblasts highly sensitive to fibrotic processes mediated via TGF-β-ERK5 interaction.2019

    • Author(s)
      Kadoya K, Togo S, Tulafu M, Namba Y, Iwai M, Watanabe J, Okabe T, Jin J, Kodama Y, Kitamura H, Ogura T, Kitamura N, Ikeo K, Takeda T, Kondo N, Takahashi K.
    • Journal Title

      Cell Physiol Biochem

      Volume: 52 Issue: 4 Pages: 822-837

    • DOI

      10.33594/000000057

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Clonal analysis revealed functional heterogeneity in cancer stem-like cell phenotypes in uterine endometrioid adenocarcinoma.2019

    • Author(s)
      Tabuchi Y, Hirohashi Y, Hashimoto S, Mariya T, Asano T, Ikeo K, Kuroda T, Mizuuchi M, Murai A, Uno S, Kawai N, Kubo T, Nakatsugawa M, Kanaseki T, Tsukahara T, Saito T, Torigoe T.
    • Journal Title

      Exp Mol Pathol

      Volume: 106 Pages: 78-88

    • DOI

      10.1016/j.yexmp.2018.11.013

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Maser: one-stop platform for NGS big data from analysis to visualization.2018

    • Author(s)
      Kinjo S, Monma N, Misu S, Kitamura N, Imoto J, Yoshitake K, Gojobori T, Ikeo K.
    • Journal Title

      Database (Oxford).

      Volume: 2018 Pages: 1-12

    • DOI

      10.1093/database/bay027

    • Related Report
      2018 Annual Research Report
    • Open Access
  • [Presentation] Reconstruction of cell lineage trees by using single-cell RNA sequence data2021

    • Author(s)
      池尾一穂
    • Organizer
      Genome Concept Centennial Conference(国立遺伝学研究所国際研究集会)
    • Related Report
      2020 Annual Research Report
  • [Remarks] Inflammatome Single Cell Data Portalサーバー

    • URL

      https://inflammation.ist.hokudai.ac.jp/

    • Related Report
      2021 Annual Research Report

URL: 

Published: 2017-07-04   Modified: 2023-01-30  

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