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

Research Project

Project/Area Number 26850024
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
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) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥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.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (13 results)

All 2016 2015 2014

All Journal Article (10 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 9 results,  Open Access: 5 results,  Acknowledgement Compliant: 4 results) Presentation (2 results) (of which Invited: 1 results) Book (1 results)

  • [Journal Article] Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling2016

    • 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

    • Related Report
      2016 Annual Research Report
    • 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

    • Related Report
      2016 Annual Research Report
    • 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: -

    • Related Report
      2015 Research-status Report
    • 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 seedlings2015

    • 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

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding2015

    • 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

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Using metabolomic approaches to explore chemical diversity in rice2015

    • 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

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis2014

    • 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

    • Related Report
      2014 Research-status Report
    • 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

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Integrated network analysis and effective tools in plant systems biology2014

    • 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

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A network perspective on nitrogen metabolism from model to crop plants using integrated “omics” approaches2014

    • Author(s)
      Atsushi Fukushima, Miyako Kusano
    • Journal Title

      Journal of Experimental Botany

      Volume: 65 Issue: 19 Pages: 5619-5630

    • DOI

      10.1093/jxb/eru322

    • Related Report
      2014 Research-status Report
    • 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
    • Related Report
      2014 Research-status Report
  • [Presentation] Let's Use R/Bioconductor and Log Your Analysis2014

    • 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
    • Related Report
      2014 Research-status Report
    • 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 Chemistry2016

    • Author(s)
      Atsushi Fukushima and Kozo Nishida
    • Total Pages
      34
    • Publisher
      Wiley
    • Related Report
      2015 Research-status Report

URL: 

Published: 2014-04-04   Modified: 2018-03-22  

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