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Analysis of robustness of metabolic networks focusing on environmental dependency of gene knockouts

Research Project

Project/Area Number 23700353
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Bioinformatics/Life informatics
Research InstitutionInstitute of Physical and Chemical Research (2013)
Ritsumeikan University (2011-2012)

Principal Investigator

TOHSATO Yukako  独立行政法人理化学研究所, 生命システム研究センター, 研究員 (80346171)

Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2012: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2011: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Keywordsバイオインフォマティクス / マイクロアレイ / 表現型 / 数理モデル / 統計解析 / 感度解析 / 代謝 / 国際情報交流 / 頑強性 / オミックスデータ解析 / 大腸菌 / 線虫 / Phenotype MicroArray / 2D-DIGE
Research Abstract

Systematic studies of genotype-phenotype correlation have revealed that most single- knockout mutants often show no observable phenotype during growth under laboratory conditions. However, such studies have mainly examined phenotypes under a limited number of conditions such as Glucose and LB mediums. Genes showing no phenotypes when absent under one condition may exhibit phenotypic changes under different specific conditions, if the gene function depends on environmental conditions. To elucidate the environmental dependency of genes, we analyzed growth data of wild-type and single-knockout mutant in Escherichia coli in 1920 medium conditions obtained from the Phenotype MicroArray. Furthermore, we develop a kinetic model for the central metabolism of E. coli that includes not only the glucose transport system, but also the glycerol transport system.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (31 results)

All 2013 2012 2011 Other

All Journal Article (12 results) (of which Peer Reviewed: 6 results) Presentation (17 results) Book (2 results)

  • [Journal Article] Parameter optimization and sensitivity analysis forlarge kinetic models using a real-coded genetic algorithm2013

    • Author(s)
      Y.Tohsato, K.Ikuta, A.Shionoya, Y.Mazaki, M .I t o
    • Journal Title

      Genes

      Volume: 518 Issue: 1 Pages: 84-90

    • DOI

      10.1016/j.gene.2012.11.080

    • Related Report
      2013 Annual Research Report 2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine2013

    • Author(s)
      Y.Matsuta, M. I to , Y. Tohsato
    • Journal Title

      Bioinformatics

      Volume: 29 Issue: 3 Pages: 365-372

    • DOI

      10.1093/bioinformatics/bts700

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Biochemical studies on sphingolipids of Artemia franciscana:complex neutral glycosphingolipids2013

    • Author(s)
      H.Kojima, Y.Tohsato, K.Kobayama, S.Itonori, M.Ito
    • Journal Title

      Glycoconjugate Journal

      Volume: 30 Issue: 3 Pages: 257-268

    • DOI

      10.1007/s10719-012-9436-8

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] 無限関係モデルを用いた大腸菌の表現型マイクロアレイ解析2013

    • Author(s)
      杉澤仁,福田一,森浩禎,谷口忠大,伊藤將弘,遠里由佳子
    • Journal Title

      立命館大学理工学研究所紀要

      Volume: 71 Pages: 49-58

    • NAID

      110009595156

    • Related Report
      2012 Research-status Report
  • [Journal Article] 無限関係モデルを用いた大腸菌の表現型マイクロアレイ解析2012

    • Author(s)
      杉澤仁,福田一,森浩禎,谷口忠大,伊藤將弘,遠里由佳子
    • Volume
      Vol.71
    • Pages
      49-58
    • NAID

      110009595156

    • URL

      http://ci.nii.ac.jp/naid/110009595156

    • Related Report
      2013 Final Research Report
  • [Journal Article] Intrinsically disordered proteins in Human mitochondria2012

    • Author(s)
      M.Ito, Y.Tohsato, H.Sugisawa, S.Kohara, S.Fukuchi, I.Nishikawa, K. Nishikawa
    • Journal Title

      Genes to Cells

      Volume: 17 Issue: 10 Pages: 817-825

    • DOI

      10.1111/gtc.12000

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Comparative proteomic analysis reveals differentially expressed proteins in Caenorhabditis eleganspgl-1 mutants grown at 20°C and 25°C2012

    • Author(s)
      Y.Tohsato, K.Monobe, K. Suzuki, T.Hayano, I.Kawasaki, M .I t o
    • Journal Title

      Journal of Proteomics

      Volume: 75 Issue: 15 Pages: 4792-4801

    • DOI

      10.1016/j.jprot.2012.04.038

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Comparative proteomic analysis reveals differentially expressed proteins igrown at 20°C and 25°Cn Caenorhabditis elegans pgl-1 mutants2012

    • Author(s)
      Yukako Tohsato, Kanami Monobe, Kenji Suzuki, Toshiya Hayano
    • Journal Title

      Journal of Proteomics

      Volume: 印刷中(掲載確定)

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] 相互情報量とSVMを用いた酵素反応におけるEC番号の推定法の開発2012

    • Author(s)
      松田祥彦, 伊藤將弘, 遠里由佳子
    • Journal Title

      立命館大学理工学研究所紀要

      Volume: 70 Pages: 21-28

    • NAID

      110009461549

    • Related Report
      2011 Research-status Report
  • [Journal Article] 線虫Caenorhabditis elegansの発生ステージにおける定量プロテオーム解析2012

    • Author(s)
      物部香奈美, 遠里由佳子, 早野俊哉, 伊藤將弘
    • Journal Title

      立命館大学理工学研究所紀要

      Volume: 70 Pages: 13-20

    • NAID

      110009461548

    • Related Report
      2011 Research-status Report
  • [Journal Article] 機械学習によるEP2受容体を標的とした化合物の探索手法の開発2011

    • Author(s)
      小原祥平, 遠里由佳子, 伊藤將弘
    • Journal Title

      情報処理学会研究報告

      Volume: 8 Pages: 1-2

    • NAID

      110008605712

    • Related Report
      2011 Research-status Report
  • [Journal Article] 相互情報量とSVMを用いた酵素反応におけるEC番号の推定手法の開発2011

    • Author(s)
      松田祥彦, 伊藤將弘, 遠里由佳子
    • Journal Title

      情報処理学会研究報告

      Volume: 7 Pages: 1-6

    • NAID

      110008605711

    • Related Report
      2011 Research-status Report
  • [Presentation] Large-Scale Kinetic Modeling for the Central Metabolism in Escherichia coli Grown on Glucose or Glycerol2013

    • Author(s)
      Akitaka Shionoya, Kunihiko Ikuta, Shuichi Onami, Masahiro Ito, Yukako Tohsato
    • Organizer
      Genome Informatics
    • Place of Presentation
      Singapore, Biopolis
    • Year and Date
      2013-12-16
    • Related Report
      2013 Final Research Report
  • [Presentation] Large-Scale Kinetic Modeling for the Central Metabolism in Escherichia coli Grown on Glucose or Glycerol2013

    • Author(s)
      Akitaka Shionoya, Kunihiko Ikuta, Shuichi Onami, Masahiro Ito, Yukako Tohsato
    • Organizer
      Genome Informatics
    • Place of Presentation
      Biopolis, Singapore
    • Related Report
      2013 Annual Research Report
  • [Presentation] Phenotype microarray analysis of Escherichia coli using infinite relational model2012

    • Author(s)
      Hitoshi Sugisawa, Hajime Fukuda, Hirotada Mori, Masahiro Ito, Tadahiro Taniguchi, Yukako Tohsato
    • Organizer
      Genome Informatics
    • Place of Presentation
      China, Hangzhou
    • Year and Date
      2012-12-12
    • Related Report
      2013 Final Research Report
  • [Presentation] Modeling of central metabolism with regulation of rpoS gene in Escherichia coli2012

    • Author(s)
      Akitaka Shionoya, Kunihiko Ikuta, Hitomi Dose, Hirotada Mori, Masahiro Ito, Yukako Tohsato
    • Organizer
      Genome Informatics
    • Place of Presentation
      China, Hangzhou
    • Year and Date
      2012-12-12
    • Related Report
      2013 Final Research Report
  • [Presentation] Parameter optimization and correlation analysis for a large kinetic model using a real-coded genetic algorithm2012

    • Author(s)
      Kunihiko Ikuta, Akitaka Shionoya, Masahiro Ito, Yukako Tohsato
    • Organizer
      Genome Informatics
    • Place of Presentation
      China, Hangzhou
    • Year and Date
      2012-12-12
    • Related Report
      2013 Final Research Report
  • [Presentation] 代謝ネットワークの頑強性に着目した数理解析2012

    • Author(s)
      遠里由佳子
    • Organizer
      電子情報通信学会2012年総合大会(招待講演)
    • Place of Presentation
      岡山大学(岡山県)
    • Related Report
      2011 Research-status Report
  • [Presentation] 遺伝子の環境依存性に着目したPhenotype MicroArray 解析2012

    • Author(s)
      遠里由佳子
    • Organizer
      第3回BKCバイオインフォマティクス研究会(招待講演)
    • Place of Presentation
      立命館大学(滋賀県)
    • Related Report
      2011 Research-status Report
  • [Presentation] Quantitative Proteomic Analysis of C. briggsae2011

    • Author(s)
      A. Terasawa, Y. Tohsato, et al.
    • Organizer
      18th International C. elegans Meeting
    • Place of Presentation
      America/University of California (Los Angeles)
    • Related Report
      2011 Research-status Report
  • [Presentation] Quantitative Proteomic Analysis in C. elegans2011

    • Author(s)
      K. Monobe, Y. Ishido, Y. Tohsato, et al.
    • Organizer
      18th International C. elegans Meeting
    • Place of Presentation
      America/University of California (Los Angeles)
    • Related Report
      2011 Research-status Report
  • [Presentation] Proteomic Analysis of C. elegans Mutants2011

    • Author(s)
      Y. Tohsato, et al.
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川都)
    • Related Report
      2011 Research-status Report
  • [Presentation] 大腸菌における表現型マイクロアレイデータ解析と数理モデルの構築

    • Author(s)
      遠里由佳子
    • Organizer
      第4回次世代創薬プロジェクトワークショップ
    • Place of Presentation
      立命館大学, 滋賀
    • Related Report
      2012 Research-status Report
  • [Presentation] Phenotype microarray analysis of Escherichia coli using infinite relational model

    • Author(s)
      Hitoshi Sugisawa, Hajime Fukuda, Hirotada Mori, Masahiro Ito, Tadahiro Taniguchi, Yukako Tohsato
    • Organizer
      The 23nd International Conference on Genome Informatic
    • Place of Presentation
      Tainan, Taiwan
    • Related Report
      2012 Research-status Report
  • [Presentation] Modeling of central metabolism with regulation of rpoS gene in Escherichia coli

    • Author(s)
      Akitaka Shionoya, Kunihiko Ikuta, Hitomi Dose, Hirotada Mori, Masahiro Ito, Yukako Tohsato
    • Organizer
      The 23nd International Conference on Genome Informatic
    • Place of Presentation
      Tainan, Taiwan
    • Related Report
      2012 Research-status Report
  • [Presentation] Parameter optimization and correlation analysis for a large kinetic model using a real-coded genetic algorithm

    • Author(s)
      Kunihiko Ikuta, Akitaka Shionoya, Masahiro Ito, Yukako Tohsato
    • Organizer
      The 23nd International Conference on Genome Informatic
    • Place of Presentation
      Tainan, Taiwan
    • Related Report
      2012 Research-status Report
  • [Presentation] Analysis of the phylogenetic profile of human glycosyltransferases

    • Author(s)
      Takayoshi Tomono, Yukako Tohsato, Masahiro Ito
    • Organizer
      The 23nd International Conference on Genome Informatic
    • Place of Presentation
      Tainan, Taiwan
    • Related Report
      2012 Research-status Report
  • [Presentation] Comparative proteomic analysis for Caenorhabditis elegans pgl-1 mutants grown at 20°C and 25°C using 2D-DIGE

    • Author(s)
      Yukako Tohsato, Kanami Monobe, Kenji Suzuki, Toshiya Hayano, Ichiro Kawasaki, Masahiro Ito
    • Organizer
      5th East Asia C. elegans Meeting
    • Place of Presentation
      Taipei, Taiwan
    • Related Report
      2012 Research-status Report
  • [Presentation] Quantitative analysis of mRNA expression profiles of ceramide-related genes using qRT-PCR

    • Author(s)
      Haruka Yamaji, Kousuke Hori, Emiko Watase, Yukako Tohsato, Kenji Suzuki, Masahiro Ito
    • Organizer
      5th East Asia C. elegans Meeting
    • Place of Presentation
      Taipei, Taiwan
    • Related Report
      2012 Research-status Report
  • [Book] Protein Function Prediction for Omics Era: 15. Towards elucidation of the Escherichia coli K-12 unknowneome2011

    • Author(s)
      Yukako Tohsato, Natsuko Yamamoto, Toru Nakayshiki, Rikiya Takeuchi, Barry L. Wanner, Hirotada Mori, Daisuke Kihara (Ed.)
    • Publisher
      Springer
    • Related Report
      2013 Final Research Report
  • [Book] Springer2011

    • Author(s)
      Y. Tohsato, et al.
    • Publisher
      Towards elucidation of the E. coli unknowneome
    • Related Report
      2011 Research-status Report

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Published: 2011-08-05   Modified: 2019-07-29  

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