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Bioinformatics using non-metric multidimensional scaling method

Research Project

Project/Area Number 19500254
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionChuo University

Principal Investigator

TAGUCHI Yoshihiro  Chuo University, 理工学部, 教授 (30206932)

Co-Investigator(Kenkyū-buntansha) OYAMA Tokitaka  京都大学, 大学院・理学研究科, 准教授 (30324396)
Project Period (FY) 2007 – 2008
Project Status Completed (Fiscal Year 2008)
Budget Amount *help
¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Fiscal Year 2008: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2007: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords非計量多次元尺度構成法 / ゲノム科学 / マイクロアレイ / Barcode of Life / DNA copy number異状 / プロテオミクス / シアノバクテリア / 概日周期 / DNA copy number 異常 / 分裂酵母 / 細胞分裂周期 / DNA copy number variation
Research Abstract

近年、遺伝子に関する網羅的な実験結果が広く公開される様になってきた。本研究では数千個の遺伝子に対して行われた遺伝子発現、蛋白質発現、塩基配列、アミノ酸配列などのデータを非計量多次元尺度構成法を用いて解析して、遺伝子の機能などを解明する研究を行った。この結果、この様な様々なデータに対して、非計量多次元尺度構成法を用いた研究が非常に有効であることを確認した。

Report

(3 results)
  • 2008 Annual Research Report   Final Research Report ( PDF )
  • 2007 Annual Research Report
  • Research Products

    (45 results)

All 2009 2008 2007 Other

All Journal Article (17 results) (of which Peer Reviewed: 6 results) Presentation (21 results) Book (4 results) Remarks (3 results)

  • [Journal Article] Analysis of DNA copy number alterations with non-metric multidimensional scaling method2008

    • Author(s)
      Fumiaki Kataoka, Y-h. Taguchi
    • Journal Title

      PSJ SIG Technical Report 2008-BIO-12

      Pages: 55-62

    • NAID

      110006824832

    • Related Report
      2008 Final Research Report
  • [Journal Article] Gene Ontology Term Prediction Based upon Amino Acid Occurrence2008

    • Author(s)
      Y-h. Taguchi, M. Michael Gromiha
    • Journal Title

      2008 International Joint Conference on Neural Networks

      Pages: 616-621

    • Related Report
      2008 Annual Research Report 2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cancer discrimination based upon non-metric multidimensional scaling method2008

    • Author(s)
      Masaru Konno, Y-h. Taguchi
    • Journal Title

      IPSJ SIG Technical Report 2008-BIO-13

      Pages: 13-16

    • NAID

      110006839042

    • Related Report
      2008 Final Research Report
  • [Journal Article] Markov random field models for protein function prediction2008

    • Author(s)
      Hisamitsu Akiba, Y-h. Taguchi
    • Journal Title

      IPSJ SIG Technical Report 2008-BIO-14

      Pages: 51-54

    • NAID

      40016268107

    • Related Report
      2008 Final Research Report
  • [Journal Article] Nonmetric Distances for Barcode of Life2008

    • Author(s)
      Hisamitsu Akiba, Y-h. Taguchi
    • Journal Title

      IPSJ Transactions on Bioinformatics 1

      Pages: 35-41

    • NAID

      110006343480

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] A Novel Discrimination of GO term Annotated Proteins based on Amino Acid Occurrence and Composition, Pattern Recognition in Bioinformatics2008

    • Author(s)
      Y-h. Taguchi, M. Michael Gromiha
    • Journal Title

      Thirs IAPR Internatiocal Workshop, PRIB2008, Supplementary Proccedings

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of DNA copy number alterations with non-metric multidimensional scaling method2008

    • Author(s)
      Fumiaki Kataoka, Y-h. Taguchi
    • Journal Title

      IPSJ SIG Technical Report 2008-BIO-12

      Pages: 55-62

    • NAID

      110006824832

    • Related Report
      2008 Annual Research Report
  • [Journal Article] Cancer discrimination based upon non-metric multidimensional scaling method2008

    • Author(s)
      Masaru Konno, Y-h. Tasuchi
    • Journal Title

      IPSJ SIG Technical Report 2008-BIO-13

      Pages: 13-16

    • Related Report
      2008 Annual Research Report
  • [Journal Article] Markov random field models for protein function prediction2008

    • Author(s)
      Hisamitsu Akiba, Y-h. Taguchi
    • Journal Title

      IPST SIG Technical Report 2008-BIO-14

      Pages: 51-54

    • NAID

      40016268107

    • Related Report
      2008 Annual Research Report
  • [Journal Article] A Novel Discrimination of GO term Annotated Proteins based on Amino Acid Occurrence and Composition2008

    • Author(s)
      Y-h. Taguchi, M. Michael Gromiha
    • Journal Title

      Pattern Recognition in Bioinformatics, Thirs IAPR Internatiocal Workshop, PRIB2008, Supplementary Proceedings

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of DNA copy number alterations with non-metric multidimensional scaling method2008

    • Author(s)
      Fumiaki Kataoka, Y-h.Taguchi
    • Journal Title

      IPSJ SIG Technical Report 2008[15]

      Pages: 55-61

    • NAID

      110006824832

    • Related Report
      2007 Annual Research Report
  • [Journal Article] Nonmetric distances for Barcode of Life2007

    • Author(s)
      Hisamitsu Akiba, Y-h. Taguchi
    • Journal Title

      IPSJ SIG Technical Report 2007-BIO-9

      Pages: 31-38

    • NAID

      110006343480

    • Related Report
      2008 Final Research Report
  • [Journal Article] A robust measure of correlation between two genes on a microarray using non-metric multidimensional scaling method2007

    • Author(s)
      Y-h. Taguchi
    • Journal Title

      IPSJ SIG Technical Report 2007-BIO-10

      Pages: 1-8

    • Related Report
      2008 Final Research Report
  • [Journal Article] Protein Fold Recognition based upon the Amino Acid Occurrence2007

    • Author(s)
      Y-h. Taguchi, M. Michael Gromiha
    • Journal Title

      Pattern Recognition in Bioinformatics, Second IAPR Internatiocal WorkshopWorkshop, PRIB2007, Proccedings, Springer 4774

      Pages: 120-131

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Application of amino acid occurrence for discriminating different folding types of globular protein2007

    • Author(s)
      Y-h. Taguchi, MM Gromiha
    • Journal Title

      BMC Bioinformatics 8

      Pages: 404-404

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] A robust measure of correlation between two genes on a microarray using non-metric multidimensional scaling method2007

    • Author(s)
      Y-h.Taguchi
    • Journal Title

      IPSJ SIG Technical Report 2007[89]

      Pages: 1-8

    • Related Report
      2007 Annual Research Report
  • [Journal Article] Nonmetric distances for Barcode of Life2007

    • Author(s)
      Hisamitsu Akiba, Y-h.Taguchi
    • Journal Title

      IPSJ SIG Technical Report 2007[60]

      Pages: 31-38

    • NAID

      110006343480

    • Related Report
      2007 Annual Research Report
  • [Presentation] 非計量多次元尺度構成法の生体生命情報学への応用2008

    • Author(s)
      田口善弘
    • Organizer
      バイオアカデミックフォーラム
    • Place of Presentation
      東京
    • Year and Date
      2008-07-03
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Presentation] GO Term Prediction for UniProt Using Amino Acid Occurrence (invited)2008

    • Author(s)
      Y-h. Taguchi
    • Organizer
      Pepcon2008 : Peptide & Protein Technology : From Concept to Market
    • Place of Presentation
      深セン
    • Year and Date
      2008-04-22
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Presentation] nMDSを使ったマイクロアレイデータとプロテオミクスデータの比較2008

    • Author(s)
      廣瀬綾子, 田口善弘
    • Organizer
      第18回システムバイオロジー研究会
    • Place of Presentation
      東京
    • Year and Date
      2008-03-14
    • Related Report
      2008 Final Research Report
  • [Presentation] 非計量多次元尺度構成法の生体生命情報解析への応用2008

    • Author(s)
      田口 善弘
    • Organizer
      第36回分子生物情報研究会(SIG-MBI)人工知能学会
    • Place of Presentation
      理化学研究所 横浜研究所
    • Year and Date
      2008-01-11
    • Related Report
      2007 Annual Research Report
  • [Presentation] 非計量多次元尺度構成法の生体生命情報解析への応用2008

    • Author(s)
      田口善弘
    • Organizer
      第36回分子生物情報研究会(SIG-MBI)
    • Place of Presentation
      東京
    • Year and Date
      2008-01-01
    • Related Report
      2008 Final Research Report
  • [Presentation] Cancer discrimination based upon non-metric multidimensional scaling method2008

    • Author(s)
      Masaru Konno, Y-h. Taguchi
    • Organizer
      16th Annual International Conference Intelligent Systems for Molecular Biology
    • Place of Presentation
      Tront
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Presentation] Analysis of DNA copy number alterations with non-metric multidimensional scaling method2008

    • Author(s)
      umiaki Kataoka, Y-h. Taguchi
    • Organizer
      16th Annual International Conference Intelligent Systems for Molecular Biology
    • Place of Presentation
      Tront
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Presentation] Markov random field models for protein function prediction2008

    • Author(s)
      Hisamitsu Akiba, Y-h. Taguchi
    • Organizer
      16th Annual International Conference Intelligent Systems for Molecular Biology
    • Place of Presentation
      Tront
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Presentation] ESTIMATION OF CELL CYCLE REGULATED GENES USING ANCHOR GENES AND NON-METRIC MULTIDIMENSIONAL SCALING2008

    • Author(s)
      Y-h. Taguchi
    • Organizer
      16th Annual International Conference Intelligent Systems for Molecular Biology
    • Place of Presentation
      Tront
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Presentation] Estimation of cell cycle regulated genes using anchor genes and non-metric multidimensional scaling2008

    • Author(s)
      Y-h. Taguchi
    • Organizer
      The Sixth Asia Pacific Bioinformatics Conference
    • Place of Presentation
      京都
    • Related Report
      2008 Final Research Report
  • [Presentation] Analysis of DNA copy number alterations with non-metric multidimensional scaling method2008

    • Author(s)
      Fumiaki Kataoka, Y-h. Taguchi
    • Organizer
      The Sixth Asia Pacific Bioinformatics Conference
    • Place of Presentation
      京都
    • Related Report
      2008 Final Research Report
  • [Presentation] Analysis of DNA copy number alterations with non-metric multidimensional scaling method2007

    • Author(s)
      Fumiaki Kataoka, Y-h. Taguchi
    • Organizer
      The 2007 Annual Conference of Japanese Society for Bioinformatics
    • Place of Presentation
      東京
    • Year and Date
      2007-12-17
    • Related Report
      2008 Final Research Report
  • [Presentation] Estimation of cell cycle regulated genes using anchor genes and non-metric multidimensional scaling2007

    • Author(s)
      Y-h. Taguchi
    • Organizer
      The 2007 Annual Conference of Japanese Society for Bioinformatics
    • Place of Presentation
      東京
    • Year and Date
      2007-12-17
    • Related Report
      2008 Final Research Report
  • [Presentation] 非計量多次元尺度構成法とその生体生命情報解析への応用2007

    • Author(s)
      田口善弘
    • Organizer
      統計数理研究所研究会非線形科学と統計科学の対話
    • Place of Presentation
      東京
    • Year and Date
      2007-11-27
    • Related Report
      2008 Final Research Report
  • [Presentation] 非計量多次元尺度構成法を用いた生体生命情報解析2007

    • Author(s)
      田口善弘
    • Organizer
      バイオアカデミックフォーラム
    • Place of Presentation
      東京
    • Year and Date
      2007-06-21
    • Related Report
      2008 Final Research Report
  • [Presentation] Nonmetric Distance for Barcode of Life2007

    • Author(s)
      Hisamitsu Akiba,Y-h. Taguchi
    • Organizer
      Second IAPR Internatiocal Workshop, PRIB2007
    • Place of Presentation
      Singapore
    • Related Report
      2008 Final Research Report
  • [Presentation] Gene Arrangement for Cell Division Cycle Microarray Experiments without Sinusoidal Fittings2007

    • Author(s)
      Kazuhisa Makabe, Y-h. Taguchi
    • Organizer
      Second IAPR Internatiocal Workshop, PRIB2007
    • Place of Presentation
      Sigapore
    • Related Report
      2008 Final Research Report
  • [Presentation] Gene arrangement for cell division cycle microarray experiments without sinusoidal fittings2007

    • Author(s)
      Kazuhisa Makabe, Y-h. Taguchi
    • Organizer
      Eleventh Annual International Conference on Research in Computational Molecura Biology
    • Place of Presentation
      サンフランシスコ
    • Related Report
      2008 Final Research Report
  • [Presentation] Gene expression profile analysis for circadian promoter activities of cyanobacterial bioluminescent reporter strains using non-metric multidimensional scaling2007

    • Author(s)
      Tokitaka Oyama, Hiroshi Ito, Takao Kondo, Y-h. Taguchi
    • Organizer
      Eleventh Annual International Conference on Research in Computational Molecura Biology
    • Place of Presentation
      サンフランシスコ
    • Related Report
      2008 Final Research Report
  • [Presentation] Nonmetric distances for Barcode of Life2007

    • Author(s)
      Hisamitsu Akiba, Y-h. Taguchi
    • Organizer
      Eleventh Annual International Conference on Research in Computational Molecura Biology
    • Place of Presentation
      サンフランシスコ
    • Related Report
      2008 Final Research Report
  • [Presentation] Recognition of protein folds using amino acid occurrence2007

    • Author(s)
      Y-h. Taguchi, M. Michael Gromiha
    • Organizer
      Eleventh Annual International Conference on Research in Computational Molecura Biology
    • Place of Presentation
      サンフランシスコ
    • Related Report
      2008 Final Research Report
  • [Book] The Kai Oscillator In "Bacterial circadian clock and rhythms book". Edited by Johnson CH, Mackey SR, Ditty JL2009

    • Author(s)
      T. Oyama, T. Kondo
    • Publisher
      Springer Publishing New York(in press)
    • Related Report
      2008 Final Research Report
  • [Book] 高校で教わりたかった物理2009

    • Author(s)
      田口善弘
    • Total Pages
      170
    • Publisher
      日本評論社
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Book] The Kai Oscillator in “Bacterial circadian clock and rhythms book"2009

    • Author(s)
      T. Oyama, T. Kondo, (Edited by Johnson CH, Mackey SR, Ditty JL. )
    • Publisher
      Springer Publishing New York(in press)
    • Related Report
      2008 Annual Research Report
  • [Book] 文庫で読む科学2007

    • Author(s)
      田口善弘
    • Publisher
      岩波書店
    • Related Report
      2008 Final Research Report
  • [Remarks] 田口善弘, 非計量多次元尺度構成法とその生体生命情報解析への応用, 物性研究, 91, pp.137-143(2008)

    • Related Report
      2008 Final Research Report
  • [Remarks] 伊庭幸人、末谷大道、青柳富誌生、田口善弘、小松崎民樹, 研究会報告「非線型科学と統計科学の対話」, 91, pp.113-174,(2008)

    • Related Report
      2008 Final Research Report
  • [Remarks] 田口善弘、フロ桶はいついっぱいになる?、数学セミナー、9月号、pp.44-47,(2007)

    • Related Report
      2008 Final Research Report

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Published: 2007-04-01   Modified: 2016-04-21  

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