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Development of methods for quantitative description and perturbation of biomolecular pathways and networks

Research Project

Project/Area Number 17017004
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo

Principal Investigator

ITO Takashi  The University of Tokyo, 大学院・理学系研究科, 教授 (90201326)

Co-Investigator(Kenkyū-buntansha) SUMIMOTO Hideki  九州大学, 大学院・医学系研究科, 教授 (30179303)
KITO Keiji  明治大学, 農学部, 講師 (40345632)
Project Period (FY) 2005 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥104,000,000 (Direct Cost: ¥104,000,000)
Fiscal Year 2009: ¥21,700,000 (Direct Cost: ¥21,700,000)
Fiscal Year 2008: ¥21,600,000 (Direct Cost: ¥21,600,000)
Fiscal Year 2007: ¥21,400,000 (Direct Cost: ¥21,400,000)
Fiscal Year 2006: ¥21,100,000 (Direct Cost: ¥21,100,000)
Fiscal Year 2005: ¥18,200,000 (Direct Cost: ¥18,200,000)
Keywords転写開始点 / 次世代シーケンサ / 定量プロテオミクス / ユビキチン化 / FRET / 遺伝子発現 / GIS-PET / ゲノム / トランスクリプトーム / プロテオーム / 定量性 / 454シークエンサ / 非コードRNA / 安定同位元素標識 / 質量分析 / 代謝物 / 蛋白質問相互作用 / リン酸化 / 質最分析 / 定量 / 蛋白質間相互作用
Research Abstract

As a basis for understanding dynamics of biomolecular pathways and networks, we developed novel methods for absolute quantification of gene expression using next generation DNA sequencing, absolute quantification of protein-protein interactions and quantitative analysis of ubiquitinated proteomes by mass spectrometry, and real-time monitoring of intracellular metabolites using FRET.

Report

(6 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • Research Products

    (34 results)

All 2010 2009 2008 2007 2006 2005

All Journal Article (28 results) (of which Peer Reviewed: 19 results) Presentation (3 results) Book (3 results)

  • [Journal Article] Remodeling of the SCF complex-mediated ubiquitination system by compositional alteration of incorporated F-box proteins2010

    • Author(s)
      Kato, M., Kito, K., Ota, K., Ito, T.
    • Journal Title

      Proteomics 10

      Pages: 115-123

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Remodeling of the SCF complex-mediated ubiquitination system by compositional alteration of incorporated F-box proteins.2010

    • Author(s)
      Kato, M., et al.
    • Journal Title

      Proteomics

      Volume: 10 Pages: 115-123

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor2009

    • Author(s)
      Okada, S., Ota, K., Ito, T.
    • Journal Title

      Protein Sci. 18

      Pages: 2518-2527

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor.2009

    • Author(s)
      Okada, S., et al.
    • Journal Title

      Protein Science

      Volume: 18 Pages: 2518-2527

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs2008

    • Author(s)
      Miura, F., Kawaguchi, N., Yoshida, M., Uematsu, C., Kito, K., Sakaki, Y., Ito, T.
    • Journal Title

      BMC Genomics 9

      Pages: 574-574

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A proteomic screen reveals the mitochondrial outer membrane protein Mdm34p as an essential target of the F-box protein Mdm30p2008

    • Author(s)
      Ota, K., Kito, K., Okada, S., Ito, T.
    • Journal Title

      Genes Cells 13

      Pages: 1075-1085

    • Related Report
      2009 Final Research Report 2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Unexpected complexity of the budding yeast transcriptome2008

    • Author(s)
      Ito, T., Miura, F., Onda, M.
    • Journal Title

      IUBMB Life 60

      Pages: 775-781

    • Related Report
      2009 Final Research Report 2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mass spectrometry-based approaches toward absolute quantitative proteomics2008

    • Author(s)
      Kito, K., Ito, T.
    • Journal Title

      Curr.Genomics 9

      Pages: 263-274

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A parallel affinity purification method for selective isolation of polyubiquitinated proteins2008

    • Author(s)
      Ota, K., Kito, K., Iemura, S., Natsume, T, Ito, T.
    • Journal Title

      Proteomics 8

      Pages: 3004-3007

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomics2008

    • Author(s)
      Kito, K., Kawaguchi, N., Okada, S., Ito, T.
    • Journal Title

      Proteomics 8

      Pages: 2366-2370

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A parallel affinity purification method for selective isolation of polyubiquitinated proteins2008

    • Author(s)
      Ota, K., Kito, K., Iemura, S., Natsume, T., Ito, T.
    • Journal Title

      Proteomics 8

      Pages: 3004-3007

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Absolute quantification of budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs2008

    • Author(s)
      Miura, F., Kawaguchi, N., Yoshida, M., Uematsu, C., Kito, K., Sakaki, Y., Ito, T.
    • Journal Title

      BMC Genomics 9

      Pages: 574-574

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mass spectrometry-based approaches toward absolute quantitative proteomics2008

    • Author(s)
      Kito, K., Ito, T.
    • Journal Title

      Curr. Genomics 9

      Pages: 263-274

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure and function of the PB1 domain, a protein-interaction module conserved in animals, fungi, amoebas, and plants2007

    • Author(s)
      Sumimoto, H., Kamakura, S., Ito, T.
    • Journal Title

      Sci.STKE 2007

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes2007

    • Author(s)
      Kito, K., Ota, K., Fujita, T., Ito, T.
    • Journal Title

      J.Proteome Res. 6

      Pages: 792-800

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A novel Cdc42-interacting domain of the yeast polarity establishment protein Beml : implications for modulation of mating pheromone signaling2007

    • Author(s)
      Yamaguchi, Y., Ota, K., Ito, T.
    • Journal Title

      J.Biol.Chem. 282

      Pages: 29-38

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure and function of the PB1 domain, a protein-interaction module conserved in animals, fungi, amoebas, and plants2007

    • Author(s)
      Sumimoto, H., Kamakura, S., & Ito, T.
    • Journal Title

      Science's STKE 2007

    • Related Report
      2007 Annual Research Report
  • [Journal Article] Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomics2007

    • Author(s)
      Kito, K., Kawaguchi, N., Okada, S., & Ito, T.
    • Journal Title

      Proteomics 8(12)

      Pages: 2366-2370

    • Related Report
      2007 Annual Research Report
  • [Journal Article] A novel, Cdc42-interacting domain of the yeast polarity establishment protein Bem1 : implications for modulation of mating pheromone signaling.2007

    • Author(s)
      Yamaguchi, Y., Ota, K., Ito, T.
    • Journal Title

      J. Biol. Chem. 282

      Pages: 29-38

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes.2007

    • Author(s)
      Kito, K., Ota, K., Fujita, T., Ito, T.
    • Journal Title

      J. Proteome Res. 6

      Pages: 792-800

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A large-scale full-length cDNA analysis to explore the budding yeast transcriptome2006

    • Author(s)
      Miura, F., Kawaguchi, N., Sese, J., Toyoda, A., Hattori, M., Morishita, S., Ito, T.
    • Journal Title

      Proc.Natl.Acad.Sci.USA 103

      Pages: 17846-17851

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Transcriptional activators in yeast2006

    • Author(s)
      Titz, B., Thomas, S., Rajagopala, S., Chiba, T., Ito, T., Uetz, P.
    • Journal Title

      Nucleic Acids Res. 34

      Pages: 955-967

    • Related Report
      2009 Final Research Report 2005 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 11q : comparison with chromosome 21q.2006

    • Author(s)
      Yamada, Y., ShiraKawa T., Taylor, T., Okamura, K., Soejima, H., Uchiyama, M., Iwasaka, T., Mukai, T., Muramoto, K., Sakaki, Y., Ito, T.
    • Journal Title

      DNA Seq. 17(3)

      Pages: 300-306

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Diverse DNA methylation status at alternative promoters of human genes in various normal tissues.2006

    • Author(s)
      Cheong, J., Yamada, Y., Yamashita, R., Irie, T., Kanai, A., Wakaguri, H., Nakai, K., Ito, T., Saito, I., Sugano, S., Suzuki, Y.
    • Journal Title

      DNA Res. 13

      Pages: 155-167

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.2006

    • Author(s)
      Miura, F., Kawaguchi, N., Sese, J., Toyoda, A., Hattori, M., Morishita, S., Ito, T.
    • Journal Title

      Proc. Natl. Acad. Sci. USA 103

      Pages: 17846-17851

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Lessons from comparative analysis of species-specific imprinted genes2006

    • Author(s)
      Okamura, K., Ito, T.
    • Journal Title

      Cytogenet.Genome Res. 113(印刷中)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3' -end subsequences2005

    • Author(s)
      Miura, F., Uematsu, C., Sakaki, Y., Ito, T.
    • Journal Title

      Bioinformatics 21

      Pages: 4363-4370

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequences2005

    • Author(s)
      Miura, E, Uematsu, C., Sakaki, Y., Ito, T.
    • Journal Title

      Bioinformatics 21

      Pages: 4363-4370

    • Related Report
      2005 Annual Research Report
  • [Presentation] ペプチド連結型標準物質と質量分析(PCS-MS法)を用いたタンパク質の絶対量計測技術の開発2009

    • Author(s)
      紀藤圭治、伊藤隆司
    • Organizer
      日本ヒトプロテオーム機構第7回大会
    • Place of Presentation
      東京、北里大学薬学部
    • Related Report
      2009 Annual Research Report
  • [Presentation] Unexpected complexity of the budding yeast transcriptome2008

    • Author(s)
      Takashi Ito
    • Organizer
      ASBMB (American Society of Biochemistry and Molecular Biology) 2008
    • Place of Presentation
      Symposium "Global Systems Biology : Parts" SanDiego
    • Year and Date
      2008-04-06
    • Related Report
      2009 Final Research Report
  • [Presentation] Unexpected complexity of the budding yeast transcriptome2008

    • Author(s)
      Takashi Ito
    • Organizer
      ASBMB2008
    • Place of Presentation
      San Diego, USA
    • Year and Date
      2008-04-06
    • Related Report
      2008 Annual Research Report
  • [Book] 明日を拓く新次元プロテオミクス(松本雅記、中山敬一:編)2009

    • Author(s)
      紀藤圭治、伊藤隆司
    • Total Pages
      144
    • Publisher
      学研メディカル秀潤社
    • Related Report
      2009 Annual Research Report
  • [Book] Methods for protein-protein interaction analysis, Introduction to Systems Biology(Ed.Choi, S.)2007

    • Author(s)
      Kito, K., Ito, T.
    • Publisher
      Humana Press
    • Related Report
      2009 Final Research Report
  • [Book] Introduction to Systems Biology, Chapter 9 : Methods for Protein-Protein Interaction Analysis2007

    • Author(s)
      Kito, K. & Ito, T.
    • Publisher
      Humana Press
    • Related Report
      2007 Annual Research Report

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Published: 2005-04-01   Modified: 2018-03-28  

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