Development of gene-function prediction models with highly predictive and sustainable construction by integrated network analysis
| Project/Area Number |
17K07663
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Horticultural science
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| Research Institution | Institute of Physical and Chemical Research |
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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)
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| Project Period (FY) |
2017-04-01 – 2020-03-31
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| Project Status |
Completed (Fiscal Year 2019)
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| 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)
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| 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 |
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| 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.
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| 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)。
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Report
(4 results)
Research Products
(22 results)
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[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
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Journal Title
Proceedings of the National Academy of Sciences of the United States of America
Volume: 115
Issue: 34
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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[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
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Journal Title
Scientific Reports
Volume: 印刷中
NAID
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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[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
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Journal Title
Nature Plants
Volume: 3
Issue: 7
Pages: 17097-17097
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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