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

• Project/Area Number: 17K07663
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Horticultural science
• Research Institution: Institute 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: ¥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)。

Research Products

• [Journal Article] Cytosolic GLUTAMINE SYNTHETASE1;1 Modulates Metabolism and Chloroplast Development in Roots (2020)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress (2020)
  • 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
  • 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
  • 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 tomato (2019)
  • 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
  • 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
  • Open Access
• [Journal Article] Application of Quantum Chemical Calculation for Prediction of Ultraviolet-vis Spectrum of Plant Self-protective MetabolitesProduced by UV-B Irradiation (2019)
  • 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
  • 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 Treatments (2018)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Third DWF1 paralog in Solanaceae, sterol Δ24-isomerase, branches withanolide biosynthesis from the general phytosterol pathway (2018)
  • 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
  • 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 Stress (2018)
  • 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
  • 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 Network (2018)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs (2018)
  • 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
  • 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 Network (2018)
  • Author(s): Yasunori Ichihashi, Atsushi Fukushima, Arisa Shibata, Ken Shirasu
  • Journal Title: Methods in Molecular Biology Volume: 印刷中
• [Journal Article] eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice (2017)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Acetate-mediated novel survival strategy against drought in plants (2017)
  • 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
  • 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 thaliana (2017)
  • 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
  • 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
• [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）
  • Invited
• [Presentation] MSEAp: Development of a metabolite set enrichment analysis toolkit for plant metabolomics community (2018)
  • 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
• [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
• [Presentation] RIKEN Plant Metabolome MetaDatabase: An integrated plant metabolome data repository based on the semantic web (2018)
  • Author(s): Atsushi Fukushima, Mikiko Takahashi, Nozomu Sakurai, Toshiaki Tokimatsu, Hideki Nagasaki, Hideki Hirakawa, Takeshi Ara, Masanori Arita, Norio Kobayashi
  • Organizer: SWAT4HCLS 2018
  • 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/
• [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/