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Development of gene-function prediction models with highly predictive and sustainable construction by integrated network analysis

Research Project

Project/Area Number 17K07663
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Horticultural science
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Fukushima Atsushi  国立研究開発法人理化学研究所, 環境資源科学研究センター, 研究員 (80415281)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2019: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2017: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Keywordsバイオインフォマティクス / 園芸ゲノム科学 / 園芸ゲノム科学・バイオインフォマティクス
Outline of Final Research Achievements

This study tried to integrate existing knowledge related to gene functions and correlation-based biomolecular networks using different types of omics data for deeper understanding a genotype-environment interaction in physiological events of plants. The results include (i) advanced development of gene-function prediction methods with high predictive accuracy by integrating omics data and (ii) evaluation of correlation networks constructed by Pearson correlation coefficient and information-theoretic inference methods. We developed the method to quantify and predict gene-gene functional links. By using the developed method, we performed differential regulation analysis (DRA) to predict candidate regulators based on differential co-expression data.

Academic Significance and Societal Importance of the Research Achievements

断続的に産出されるオミックスデータに対応し、遺伝子機能予測モデルの構築を“持続的に”行うことができる統計モデルは、利用可能なオミックスデータが増えるに従って、予測精度の改善が見込まれる。このため、持続的にその構築を行うソフトウェア実装が重要となる。植物の持つ環境応答の頑健さと柔軟さとを理解するため、生理機能の背後にある遺伝子ネットワークの特性解明に大きく寄与する。本研究課題の遺伝子機能予測モデルおよび解析手法は、将来的に総合的な「環境適応型植物設計システム」の重要なモジュールの一つとなりうる(新技術の創製)。

Report

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

    (22 results)

All 2020 2019 2018 2017 Other

All Journal Article (15 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 13 results,  Open Access: 14 results) Presentation (5 results) (of which Int'l Joint Research: 1 results,  Invited: 1 results) Remarks (2 results)

  • [Journal Article] Cytosolic GLUTAMINE SYNTHETASE1;1 Modulates Metabolism and Chloroplast Development in Roots2020

    • Author(s)
      Kusano Miyako、Fukushima Atsushi、Tabuchi-Kobayashi Mayumi、Funayama Kazuhiro、Kojima Soichi、Maruyama Kyonoshin、Yamamoto Yoshiharu Y.、Nishizawa Tomoko、Kobayashi Makoto、Wakazaki Mayumi、Sato Mayuko、Toyooka Kiminori、Osanai-Kondo Kumiko、Utsumi Yoshinori、Seki Motoaki、Fukai Chihaya、Saito Kazuki、Yamaya Tomoyuki
    • Journal Title

      Plant Physiology

      Volume: 182 Issue: 4 Pages: 1894-1909

    • DOI

      10.1104/pp.19.01118

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress2020

    • Author(s)
      Fukushima Atsushi、Kuroha Takeshi、Nagai Keisuke、Hattori Yoko、Kobayashi Makoto、Nishizawa Tomoko、Kojima Mikiko、Utsumi Yoshinori、Oikawa Akira、Seki Motoaki、Sakakibara Hitoshi、Saito Kazuki、Ashikari Motoyuki、Kusano Miyako
    • Journal Title

      Metabolites

      Volume: 10 Issue: 2 Pages: 68-68

    • DOI

      10.3390/metabo10020068

    • NAID

      120007132876

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] BioHackathon 2015: Semantics of data for life sciences and reproducible research.,2020

    • Author(s)
      Vos, Katayama, Mishima et. al
    • Journal Title

      F1000Reseaech

      Volume: - Pages: 136-136

    • DOI

      10.12688/f1000research.18236.1

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Comparative co-expression network analysis extracts the <i>SlHSP70</i> gene affecting to shoot elongation of tomato2019

    • Author(s)
      Vu Nam Tuan、Kamiya Ken、Fukushima Atsushi、Hao Shuhei、Ning Wang、Ariizumi Tohru、Ezura Hiroshi、Kusano Miyako
    • Journal Title

      Plant Biotechnology

      Volume: 36 Issue: 3 Pages: 143-153

    • DOI

      10.5511/plantbiotechnology.19.0603a

    • NAID

      130007724757

    • ISSN
      1342-4580, 1347-6114
    • Year and Date
      2019-09-25
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] メタボロームデータ解析および解釈に資する可視化手法2019

    • Author(s)
      神谷 健、草野 都、福島 敦史
    • Journal Title

      CICSJ Bulletin

      Volume: 37 Issue: 3 Pages: 72

    • DOI

      10.11546/cicsj.37.72

    • NAID

      130007753679

    • ISSN
      0913-3747, 1347-2283
    • Related Report
      2019 Annual Research Report
    • Open Access
  • [Journal Article] Application of Quantum Chemical Calculation for Prediction of Ultraviolet-vis Spectrum of Plant Self-protective MetabolitesProduced by UV-B Irradiation2019

    • Author(s)
      KUWAHATA Kazuaki、SAKUMA Yui、KAWASHIMA Yukio、FUKUSHIMA Atsushi、NAGASHIMA Umpei、KUSANO Miyako、TACHIKAWA Masanori
    • Journal Title

      Journal of Computer Chemistry, Japan

      Volume: 18 Issue: 2 Pages: 108-114

    • DOI

      10.2477/jccj.2019-0002

    • NAID

      130007684613

    • ISSN
      1347-1767, 1347-3824
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A Systems Analysis With “Simplified Source-Sink Model” Reveals Metabolic Reprogramming in a Pair of Source-to-Sink Organs During Early Fruit Development in Tomato by LED Light Treatments2018

    • Author(s)
      Atsushi Fukushima, Shoko Hikosaka, Makoto Kobayashi, Tomoko Nishizawa, Kazuki Saito, Eiji Goto, Miyako Kusano
    • Journal Title

      Frontiers in Plant Science

      Volume: 9 Pages: 1439-1439

    • DOI

      10.3389/fpls.2018.01439

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Third DWF1 paralog in Solanaceae, sterol Δ24-isomerase, branches withanolide biosynthesis from the general phytosterol pathway2018

    • Author(s)
      Eva Knoch, Satoko Sugawara, Tetsuya Mori, Christian Poulsen, Atsushi Fukushima, Jesper Harholt, Yoshinori Fujimoto, Naoyuki Umemoto, Kazuki Saito
    • Journal Title

      Proceedings of the National Academy of Sciences of the United States of America

      Volume: 115 Issue: 34

    • DOI

      10.1073/pnas.1807482115

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] HEAT INDUCIBLE LIPASE1 Remodels Chloroplastic Monogalactosyldiacylglycerol by Liberating α-Linolenic Acid in Arabidopsis Leaves under Heat Stress2018

    • Author(s)
      Yasuhiro Higashi, Yozo Okazaki, Kouji Takano, Fumiyoshi Myouga, Kazuo Shinozaki, Eva Knoch, Atsushi Fukushima, Kazuki Saito
    • Journal Title

      Plant Cell

      Volume: 30 Issue: 8 Pages: 1887-1905

    • DOI

      10.1105/tpc.18.00347

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] High Impact Gene Discovery: Simple Strand-Specific mRNA Library Construction and Differential Regulatory Analysis Based on Gene Co-Expression Network2018

    • Author(s)
      Yasunori Ichihashi, Atsushi Fukushima, Arisa Shibata, Ken Shirasu
    • Journal Title

      Methods in Molecular Biology

      Volume: 1830 Pages: 163-189

    • DOI

      10.1007/978-1-4939-8657-6_11

    • ISBN
      9781493986569, 9781493986576
    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs2018

    • Author(s)
      Kazuyoshi Kitazaki, Atsushi Fukushima, Ryo Nakabayashi, Yozo Okazaki, Makoto Kobayashi, Tetsuya Mori, Tomoko Nishizawa, Sebastian Reyes-Chin-Wo, Richard W. Michelmore, Kazuki Saito, Kazuhiro Shoji, Miyako Kusano
    • Journal Title

      Scientific Reports

      Volume: 印刷中

    • NAID

      120007134064

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] High Impact Gene Discovery: Simple Strand Specific mRNA Library Construction and Differential Regulatory Analysis Based on Gene Co-expression Network2018

    • Author(s)
      Yasunori Ichihashi, Atsushi Fukushima, Arisa Shibata, Ken Shirasu
    • Journal Title

      Methods in Molecular Biology

      Volume: 印刷中

    • Related Report
      2017 Research-status Report
  • [Journal Article] eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice2017

    • Author(s)
      1.Takeshi Kuroha, Keisuke Nagai, Yusuke Kurokawa, Yoshiaki Nagamura, Miyako Kusano, Hideshi Yasui, Motoyuki Ashikari, Atsushi Fukushima
    • Journal Title

      Frontiers in Plant Science

      Volume: 8 Pages: 1753-1753

    • DOI

      10.3389/fpls.2017.01753

    • NAID

      120007134740

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Acetate-mediated novel survival strategy against drought in plants2017

    • Author(s)
      Kim JM, To TK, Matsui A, Tanoi K, Kobayashi NI, Matsuda F, Habu Y, Ogawa D, Sakamoto T, Matsunaga S, Bashir K, Rasheed S, Ando M, Takeda H, Kawaura K, Kusano M, Fukushima A, Endo TA, Kuromori T, Ishida J, Morosawa T, Tanaka M, Torii C, Takebayashi Y, Sakakibara H, Ogihara Y, Saito K, Shinozaki K, Devoto A, Seki M
    • Journal Title

      Nature Plants

      Volume: 3 Issue: 7 Pages: 17097-17097

    • DOI

      10.1038/nplants.2017.97

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Effects of Combined Low Glutathione with Mild Oxidative and Low Phosphorus Stress on the Metabolism of Arabidopsis thaliana2017

    • Author(s)
      3.Atsushi Fukushima, Mami Iwasa, Ryo Nakabayashi, Makoto Kobayashi, Tomoko Nishizawa, Yozo Okazaki, Kazuki Saito, Miyako Kusano
    • Journal Title

      Frontiers in Plant Science

      Volume: 8 Pages: 1464-1464

    • DOI

      10.3389/fpls.2017.01464

    • NAID

      120007134052

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] ディファレンシャルネットワークに基づく遺伝子機能予測2019

    • Author(s)
      福島敦史
    • Organizer
      第37回日本植物細胞分子生物学会(京都)大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 福島 敦史2019

    • Author(s)
      質量分析を用いた植物メタボロミクスデータの情報解析と共有
    • Organizer
      質量分析インフォマティクス研究会・第4回ワークショップ(2019年)
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] MSEAp: Development of a metabolite set enrichment analysis toolkit for plant metabolomics community2018

    • Author(s)
      Atsushi Fukushima and Kozo Nishida
    • Organizer
      第36回日本植物細胞分子生物学会(金沢)大会
    • Related Report
      2018 Research-status Report
  • [Presentation] 植物メタボロームデータの再解析・アノテーション高度化に向けた情報基盤整備2018

    • Author(s)
      福島 敦史, 津川裕司, 高橋みき子, 小林紀郎
    • Organizer
      第12回メタボロームシンポジウム
    • Related Report
      2018 Research-status Report
  • [Presentation] RIKEN Plant Metabolome MetaDatabase: An integrated plant metabolome data repository based on the semantic web2018

    • Author(s)
      Atsushi Fukushima, Mikiko Takahashi, Nozomu Sakurai, Toshiaki Tokimatsu, Hideki Nagasaki, Hideki Hirakawa, Takeshi Ara, Masanori Arita, Norio Kobayashi
    • Organizer
      SWAT4HCLS 2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Remarks] 植物の高温耐性に寄与するリパーゼ遺伝子を発見

    • URL

      http://www.riken.jp/pr/press/2018/20180706_2/

    • Related Report
      2018 Research-status Report
  • [Remarks] アシュワガンダ薬用成分の生合成遺伝子を発見

    • URL

      http://www.riken.jp/pr/press/2018/20180807_1/

    • Related Report
      2018 Research-status Report

URL: 

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

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