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転写制御における協同性の網羅的解析

Research Project

Project/Area Number 20052021
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKyushu Institute of Technology

Principal Investigator

皿井 明倫  Kyushu Institute of Technology, 大学院・情報工学研究院, 教授 (20221286)

Project Period (FY) 2008 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥6,800,000 (Direct Cost: ¥6,800,000)
Fiscal Year 2009: ¥3,400,000 (Direct Cost: ¥3,400,000)
Fiscal Year 2008: ¥3,400,000 (Direct Cost: ¥3,400,000)
Keywords転写因子 / 遺伝子発現制御 / 蛋白質・DNA認識 / ゲノム / 協同性
Research Abstract

本年度は、以下のような項目について解析をすすめた。(1) 転写因子のターゲットの網羅的予測:昨年度に引き続き、酵母ゲノムについて、蛋白質とDNAの相互作用データ、複合体の構造データや計算機シミュレーション、従来の配列情報に基づく方法などいくつかの予測方法を組み合わせることにより、網羅的な予測を行った。また、ChIP-chipやChIP-seqのデータと組み合わせて予測結果の評価を行った。これらの実験データと予測を組み合わせることにより、より精度良くターゲットを同定することができることがわかった。(2) 転写制御領域のコンテクストの解析:ターゲット遺伝子のプロモータ上に結合する転写因子のコンテクストとターゲット遺伝子の発現や機能との関係を解析した。例として、Mafという転写因子について、ターゲット候補遺伝子群のプロモータに結合する転写因子を網羅的に予測し、Mafと他の転写因子との共起関係や転写因子間の距離などの情報をもとに、これらと遺伝子発現の実験データや機能を比較した。この結果、特定の転写因子との共起関係と遺伝子発現データや機能との間に相関を見いだすことができた。(3) 転写制御ネットワークと協同性の解析:転写制御情報のデータベースを解析することにより、転写因子とターゲット遺伝子の産物からなるネットワークを構築しつつある。また、構造情報に基づいた転写因子複合体構造ネットワークを構築し、実験データに基づくネットワークを統合しつつある。この統合した転写制御ネットワーク用いて、いくつかの転写制御系について構造レベルでの協同性を調べた。これらの例について調べた結果、協同的なDNAへの結合により特異性が上がることがわかった。

Report

(2 results)
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (43 results)

All 2009 2008 Other

All Journal Article (10 results) (of which Peer Reviewed: 10 results) Presentation (31 results) Remarks (2 results)

  • [Journal Article] A signature-based method for indexing cell cycle phase distribution from microarray profiles2009

    • Author(s)
      H.Mizuno, Yo Nakanishi, N.Ishii, A.Sarai, K.Kitada
    • Journal Title

      BMC Genomics 10

      Pages: 137-137

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] PrognoScan : a new database for meta-analysis of the prognostic value of genes2009

    • Author(s)
      H.Mizuno, K.Kitada, K.Nakai, A.Sarai
    • Journal Title

      BMC Medical Genomics 2

      Pages: 18-18

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of mono-and dinucleotide-specfic DNA-binding sites in proteins using neural networks2009

    • Author(s)
      M.Andrabi, K.Mizuguchi, A.Sarai, S.Ahmad
    • Journal Title

      BMC Struct.Biol. 9

      Pages: 30-30

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] MHC class II DR classification based on antigen-binding groove natural selection2009

    • Author(s)
      S.Takeshima, A.Sarai, A.Saitou, Y.Aida
    • Journal Title

      BMC Struct.Biol. 385

      Pages: 137-142

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Generalized Conformational Energy Function of DNA Derived from Molecular Dyamics Simulations2009

    • Author(s)
      S.Yamasaki, T.Terada, K.Shimizu, H.Kono, A.Sarai
    • Journal Title

      Nuxleic Acids Res. 37

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast2009

    • Author(s)
      M.Fernandez, S.Fujii, H.Kono, A.Sarai
    • Journal Title

      Genome Inform. 23

      Pages: 13-20

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] △G-based prediction and experimental confirmation of SYCRP1-binding sites on Synechocystis genome2008

    • Author(s)
      K. Omagari, H. Yoshimura, T. Suzuki, M. Takano, M. Ohmori, and A. Sarai
    • Journal Title

      FEBS J. 275

      Pages: 4786-4795

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] uORFs, reinitiation and alternative translation start sites in human mRNAs2008

    • Author(s)
      A.V. Kochetov, S. Ahmad, V.I. Ivanisenko, N. A. Kolchanovand A. Sarai
    • Journal Title

      FEBS Lett 582

      Pages: 1293-1297

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein-DNA interactions : Structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins2008

    • Author(s)
      S. Ahmad, O. Keskin, A. Sarai and R. Nussino V
    • Journal Title

      Nucleic Acids Res 36

      Pages: 5922-5932

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sequence-based prediction of residue-level properties in proteins2008

    • Author(s)
      S. Ahmad, Y. H. Singh, M. J. Araitzo-Bravo, A. Sarai
    • Journal Title

      Machine Learning in Bioinformatics Chap. 7

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] 生体分子の熱力学データと構造データの統合2009

    • Author(s)
      皿井明倫、Shaji Kumar
    • Organizer
      文科省統合データベースプロジェクトシンポジウム「データベースが拓くこれからのライフサイエンス」
    • Place of Presentation
      東京
    • Year and Date
      2009-06-12
    • Related Report
      2009 Annual Research Report
  • [Presentation] Protein-DNA Recognition Mechanism and Prediction2009

    • Author(s)
      A.Sarai
    • Organizer
      Albany 2009 : the 16th Conversation
    • Place of Presentation
      Albany, NY, USA
    • Related Report
      2009 Annual Research Report
  • [Presentation] Analysis of Biomolecular Network in Structurome2009

    • Author(s)
      M.Ohtsuaka, S.Fujii, Akinori Sarai
    • Organizer
      ISMB/ECCB 2009
    • Place of Presentation
      Skockholm, Sweden
    • Related Report
      2009 Annual Research Report
  • [Presentation] Stability, Dynamics and Cooperativity of Protein-DNA Interactions2009

    • Author(s)
      A.Sarai
    • Organizer
      International Symposium on Multi-Scale Dynamics of Protein Complex Formation and Function
    • Place of Presentation
      Tokyo
    • Related Report
      2009 Annual Research Report
  • [Presentation] Kinase Inhibition modeling by Proteometrics and docking analysis2009

    • Author(s)
      Michael Fernandez, Ahmad Shandar, Akinori Sarai
    • Organizer
      CBI-KSBSB Joint Conference
    • Place of Presentation
      Busan, Korea
    • Related Report
      2009 Annual Research Report
  • [Presentation] Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast2009

    • Author(s)
      M.Fernandez, S.Fujii, H.Kono, A.Sarai
    • Organizer
      GIW2009
    • Place of Presentation
      Yokohama
    • Related Report
      2009 Annual Research Report
  • [Presentation] 未構造タンパク質の機能的進化的特性:生物種特異的解析2009

    • Author(s)
      黄鶴、皿井明倫
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] ストラクチュロームにおける分子ネットワークの系統的解析2009

    • Author(s)
      Mitsuaki Ohtsuaka, Satoshi Fujii, Akinori Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] 転写因子のゲノヘスケールでのターケット予測:相互作用情報を用いた方法2009

    • Author(s)
      大庭宏明、藤井聡、皿井明倫
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] The effect of environment on the conformational transition of DNA Studied by molecular dynamics simulations2009

    • Author(s)
      Satoshi Fujii, Hidetoshi Kono, Nobuhiro Go, Akinori Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] Construction and Analysis of Biomolecular Network based on Domain Structures2009

    • Author(s)
      Yukari Hayashi, Satoshi Fujii, Akinori Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] Motif Analysis of Transcription Factors in Regulatory Region2009

    • Author(s)
      T.Sakai, S.Fujii, A.Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] 構造情報に基づく蛋白質・DNA認識における協同性の解析2009

    • Author(s)
      A.Tanaka, S.Fujii, H.Kono, A.Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] ベイズ統計学的解釈によるタンパク質-DNA認識におけるindirect readoutの評価2009

    • Author(s)
      山崎智, 福井一彦, 河野秀俊, 清水謙多郎, 皿井明倫, 寺田透
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] Kinase Inhibition modeling by Proteometrics and docking analysis2009

    • Author(s)
      Michael Fernandez, Ahmad Shandar, Akinori Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] Electric moments of RNA-binding proteins2008

    • Author(s)
      S. Ahmad and A. Sarai
    • Organizer
      ISMB2008
    • Place of Presentation
      Toronto, Canada
    • Related Report
      2008 Annual Research Report
  • [Presentation] Recognition of protease inhibition pattern using topological interaction matrix and genetic algorithm-optimized support vector machines2008

    • Author(s)
      M. Fernandez, S. Ahmad, and A. Sarai
    • Organizer
      PRIB2008
    • Place of Presentation
      Melbourne, Australia
    • Related Report
      2008 Annual Research Report
  • [Presentation] Ligand-target data modeling using Genetic Algorithm-optimized Bayesian Regularized Neural Networks and Support Vectors Machines2008

    • Author(s)
      M. Fernandez, A. Sarai and J. Caballero
    • Organizer
      IASC 2008
    • Place of Presentation
      Yokohama, Japan
    • Related Report
      2008 Annual Research Report
  • [Presentation] Analysis of environment-dependent conformational transition of DNA by molecular dynamics simulations2008

    • Author(s)
      S. Fujii, H. Kono, N. Go and A. Sarai
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] Proteometric Modeling of Protein Conformational Stability using Amino Acid Sequence Autocorrelation Vectors and Sumport Vector Machines2008

    • Author(s)
      M. Fernandez, S. Ahmad, and A. Sarai
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] Integration of Thermodynamic and Structural Data2008

    • Author(s)
      A. Sarai
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] Genome-wide prediction of target of transcriptional factor with interaction data2008

    • Author(s)
      H. Ohba, A. Sarai and S. Fujii
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] Analyses of Functional and Evolutionary Characteristics of Disordered Proteins2008

    • Author(s)
      H. Huang, and A. Sarai
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] Analysis of Biomolecular Network in Structurome2008

    • Author(s)
      M. Ohtsuka, S. Fujii and Akinori Sarai
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] A New DNA-deformation energy function taking account of the anharmonicity of the conformational distribution2008

    • Author(s)
      S. Yamasaki, T. Terada, K. Shimizu, H. Kono and A. Sarai
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] Sequence-dependent DNA deformability and hydtration studied by molecular dynamics simulations2008

    • Author(s)
      Y. Yonetani, S. Fujii, A. Sarai, H. Kono, and N. Go
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] Prediction of base-specific contacts and contact-types in DNA-binding proteins2008

    • Author(s)
      M. Andrabi, K. Mizuguchi, A. Sarai and S. Ahmad
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Related Report
      2008 Annual Research Report
  • [Presentation] Evaluation of dinucleotide intramolecular interactions on nucleosome positioning2008

    • Author(s)
      M. Fernandez, S. Fujii, H. Kono, and Akinori Sarai
    • Organizer
      日本バイオインフォマティクス学会年会
    • Place of Presentation
      大阪
    • Related Report
      2008 Annual Research Report
  • [Presentation] Role of electric moments in RNA-recognition by proteins2008

    • Author(s)
      S. Ahmad and A. Sarai
    • Organizer
      日本バイオインフォマティクス学会年会
    • Place of Presentation
      大阪
    • Related Report
      2008 Annual Research Report
  • [Presentation] ProNIT : Database Development and Integration2008

    • Author(s)
      M.D. Shaji Kumar, P. Prabakaran, M.M. Gromiha, H. Uedaira, K. Kitajima, and A. Sarai
    • Organizer
      日本バイオインフォマティクス学会年会
    • Place of Presentation
      大阪
    • Related Report
      2008 Annual Research Report
  • [Presentation] Analysis of Biomolecular Network in Structurome2008

    • Author(s)
      M. Ohtsuka, S. Fujii and Akinori Sarai
    • Organizer
      日本バイオインフォマティクス学会年会
    • Place of Presentation
      大阪
    • Related Report
      2008 Annual Research Report
  • [Remarks]

    • URL

      http://gibk26.bse.Kyutech.ac.jp/jouhou/website/index.htm

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://gibk26.bse.kyutech.ac.jp/jouhou/website/index.htm

    • Related Report
      2008 Annual Research Report

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Published: 2008-04-01   Modified: 2018-03-28  

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