in silico prediction of gene function associated with agronomically useful traits in crops using differential network analysis

• Project/Area Number: 26850024
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• 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): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2014: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
• Keywords: バイオインフォマティクス / ネットワーク解析 / 共発現解析 / 遺伝子発現調節ネットワーク / 遺伝子共発現 / ディファレンシャル共発現 / ネットワーク推定 / トマト / 統合データベース

Outline of Final Research Achievements

This study aims to develop computational prediction methods of gene function associated with agronomically useful traits in crops using differential network analysis. To this end we analyzed comparative transcriptome dataset from leaf development samples using three Solanum species exhibiting different leaf development characteristics. Our differential network approach has detected coexpression alterations for genes making up the most significantly divergent cluster, and has identified thousands of potential key gene pairs under interspecific differential regulation. We are now developing and integrating a set of R pakcages for the analysis.

Research Products

• [Journal Article] Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling (2016)
  • Author(s): Atsushi Fukushima, Michimi Nakamura, Hideyuki Suzuki, Mami Yamazaki, Eva Knoch, Tetsuya Mori, Naoyuki Umemoto, Masaki Morita, Go Hirai, Mikiko Sodeoka, and Kazuki Saito
  • Journal Title: Frontiers in Plant Science Volume: 7 Pages: 1883-1883
  • DOI: 10.3389/fpls.2016.01883
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 植物におけるオミックス統合ネットワークシステム生物学 (2016)
  • Author(s): 福島 敦史
  • Journal Title: SAR News Volume: 31 Pages: 9-16
  • Open Access / Acknowledgement Compliant
• [Journal Article] 植物科学におけるトランスクリプトーム解析の最前線 (2016)
  • Author(s): 市橋 泰範、福島 敦史
  • Journal Title: 植物科学の最前線（BSJ-Review） Volume: -
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Lack of cytosolic glutamine synthetase1;2 in vascular tissues of axillary buds caused severe reduction in their outgrowth and disorder of metabolic balance in rice seedlings (2015)
  • Author(s): Ohashi, M., Ishiyama, K., Kusano, M., Fukushima, A., Kojima, S., Hanada, A., Kanno, K., Hayakawa, T., Seto, Y., Kyozuka, J., Yamaguchi, S., Yamaya, T.
  • Journal Title: Plant J. Volume: 81 Issue: 2 Pages: 347-356
  • DOI: 10.1111/tpj.12731
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding (2015)
  • Author(s): Miyako Kusano, Ivan Baxter, Atsushi Fukushima, Akira Oikawa, Yozo Okazaki, Ryo Nakabayashi, Denise J. Bouvrette, Frederic Achard, Andrew R. Jakubowski, Joan M. Ballam, Jonathan R. Phillips, Angela H. Culler, Kazuki Saito, George G. Harrigan
  • Journal Title: Metabolomics Volume: 11 Issue: 2 Pages: 261-270
  • DOI: 10.1007/s11306-014-0702-6
  • Peer Reviewed
• [Journal Article] Using metabolomic approaches to explore chemical diversity in rice (2015)
  • Author(s): Miyako Kusano, Zhigang Yang, Yozo Okazaki, Ryo Nakabayashi, Atsushi Fukushima, Kazuki Saito
  • Journal Title: Molecular Plant Volume: 8 Issue: 1 Pages: 58-67
  • DOI: 10.1016/j.molp.2014.11.010
  • NAID: 120007130222
  • Peer Reviewed
• [Journal Article] Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis (2014)
  • Author(s): Atsushi Fukushima, Miyako Kusano, Ramon Francisco Mejia, Mami Iwasa, Makoto Kobayashi, Naomi Hayashi, Akiko Watanabe-Takahashi, Tomoko Narisawa, Takayuki Tohge, Manhoi Hur, Eve Syrkin Wurtele, Basil J. Nikolau, Kazuki Saito
  • Journal Title: Plant Physiology Volume: 165 Issue: 3 Pages: 948-961
  • DOI: 10.1104/pp.114.240986
  • Peer Reviewed / Open Access
• [Journal Article] Integrated analysis of transcriptome and metabolome of Arabidopsis albino or pale green mutants with disrupted nuclear-encoded chloroplast proteins. (2014)
  • Author(s): M. Satou, H. Enoki, A. Oikawa, D. Ohta, K. Saito, T. Hachiya, H. Sakakibara, M. Kusano, A. Fukushima, K. Saito, M. Kobayashi, N. Nagata, F. Myouga, K. Shinozaki, R. Motohashi
  • Journal Title: Plant Molecular Biology Volume: 85 Issue: 4-5 Pages: 411-428
  • DOI: 10.1007/s11103-014-0194-9
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Integrated network analysis and effective tools in plant systems biology (2014)
  • Author(s): Atsushi Fukushima, Shigehiko Kanaya, Kozo Nishida
  • Journal Title: Frontiers in Plant Science Volume: 5 Pages: 598-598
  • DOI: 10.3389/fpls.2014.00598
  • Peer Reviewed / Open Access
• [Journal Article] A network perspective on nitrogen metabolism from model to crop plants using integrated “omics” approaches (2014)
  • Author(s): Atsushi Fukushima, Miyako Kusano
  • Journal Title: Journal of Experimental Botany Volume: 65 Issue: 19 Pages: 5619-5630
  • DOI: 10.1093/jxb/eru322
  • Peer Reviewed
• [Presentation] トマト果実肥大に及ぼす代謝変動解明のためのシステム生物学的アプローチ (2014)
  • Author(s): 福島敦史, 西澤 具子, 小林 誠, 彦坂 晶子, 後藤 英司, 斉藤 和季, 草野 都
  • Organizer: 第32回日本植物細胞分子生物学会大会
  • Place of Presentation: アイーナ (いわて県民情報交流センター) (岩手県盛岡市)
  • Year and Date: 2014-08-21 – 2014-08-22
• [Presentation] Let's Use R/Bioconductor and Log Your Analysis (2014)
  • Author(s): Atsushi Fukushima
  • Organizer: the 10th International conference of the Metabolomics Society (Metabolomics 2014)
  • Place of Presentation: Marica/Washington Hotel (山形県鶴岡市)
  • Year and Date: 2014-06-23
  • Invited
• [Book] Chapter 1 "Using the DiffCorr Package to Analyze and Visualize Differential Correlations in Biological Networks" In: Dehmer, Shi, Emmert-Streib, editors. Computational Network Analysis with R - Applications in Biology, Medicine and Chemistry (2016)
  • Author(s): Atsushi Fukushima and Kozo Nishida
  • Total Pages: 34
  • Publisher: Wiley