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A method for exhaustive similarity search of genomic positional expression.

Research Project

Project/Area Number 19700275
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Bioinformatics/Life informatics
Research InstitutionOsaka University

Principal Investigator

SENO Shigeto  Osaka University, 大学院・情報科学研究科, 助教 (30432462)

Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥3,860,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥660,000)
Fiscal Year 2009: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2008: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2007: ¥1,000,000 (Direct Cost: ¥1,000,000)
Keywords生物情報学 / 類似構造探索 / トランスクリプトーム解析 / 発現プロファイル / ゲノム / 類似構造検索
Research Abstract

I carried out analyses of gene expression patterns using the cap analysis gene expression (CAGE) method for exploring systematic views of tanscriptomes. Counting the number of mapped CAGE tags for fixed-length regions allows determination of the genomic expression levels. I developed a novel algorithm which provides a novel view to the genome from the genomic positional expression, and also developed a method based on graph algorithm and statistical approach for discovering tissue-specific regulation of alternative transcripts through a genome-wide analysis.

Report

(4 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (14 results)

All 2010 2009 2008 2007 Other

All Journal Article (6 results) (of which Peer Reviewed: 4 results) Presentation (8 results)

  • [Journal Article] Improved prediction method for protein interactions using both structural and functional characteristics of proteins2010

    • Author(s)
      Tatsuya Yoshikawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Journal Title

      IPSJ Transactions on Bioinformatics vol.3

      Pages: 10-23

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Improved prediction method for protein interactions using both structural and functional characteristics of proteins2010

    • Author(s)
      Tatsuya Yoshikawa
    • Journal Title

      IPSJ Transactions on Bioinformatics 3

      Pages: 10-23

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Combination Method of the Tanimoto Coefficient and Proximity Measure of Random Forest for Compound Activity Prediction2008

    • Author(s)
      Gen Kawamura, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Journal Title

      IPSJ Transactions on Bioinformatics Vol.49No.SIG5

      Pages: 46-57

    • NAID

      110006824830

    • Related Report
      2009 Final Research Report
  • [Journal Article] A Distributed-Processing System for Accelerating Biological Research using Data-Staging2008

    • Author(s)
      Yoshiyuki Kido, Shigeto Seno, Susumu Date, Yoichi Takenaka, Hideo Matsuda
    • Journal Title

      IPSJ Transactions on Bioinformatics Vol.49,No.SIG5

      Pages: 58-64

    • Related Report
      2009 Final Research Report
  • [Journal Article] A Distributed-Processing System for Accelerating Biological Research using -Staging

    • Author(s)
      Yoshiyuki Kido
    • Journal Title

      IPSJ Transactions on Bioinformatics In press

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Combination Method of the Tanimoto Coefficient arid Proximity Measure of Random Forest for Compound Activity Prediction

    • Author(s)
      Gen Kawamura
    • Journal Title

      IPSJ Thfansactions on Bioinformatics In press

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] An approach for efficient computational analysis of massive RNA-Seq data2009

    • Author(s)
      石川元一, 瀬尾茂人, 竹中要一, 松田秀雄
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2009-12-11
    • Related Report
      2009 Final Research Report
  • [Presentation] An approach for efficient computational analysis of massive RNA-Sea data2009

    • Author(s)
      石川元一
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川県)
    • Year and Date
      2009-12-11
    • Related Report
      2009 Annual Research Report
  • [Presentation] A method for analyzing gene expression profiles based on the underlying structures2009

    • Author(s)
      Shigeto Seno
    • Organizer
      International Conference on Intelligent Systems for Molecular Biology (ISMB2009)
    • Place of Presentation
      Stockholm, Sweden
    • Year and Date
      2009-06-29
    • Related Report
      2009 Annual Research Report
  • [Presentation] A method for analysis of tissue-specific alternative transcripts using CAGE tags2008

    • Author(s)
      Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      Intelligent Systems for Molecular Biology (ISMB2008)
    • Place of Presentation
      Toronto, Canada
    • Year and Date
      2008-07-21
    • Related Report
      2009 Final Research Report
  • [Presentation] A Clustering Method for Expression Patterns of Transcription Starting Sites2008

    • Author(s)
      Mitsuru Jikeya, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      Intelligent Systems for Molecular Biology (ISMB2008)
    • Place of Presentation
      Toronto, Canada
    • Year and Date
      2008-07-21
    • Related Report
      2009 Final Research Report
  • [Presentation] A method for analysis of tissue-specific alternative transcripts using CAGE tags2008

    • Author(s)
      Shigeto Seno
    • Organizer
      Intelligent Systems for Molecular Biology(ISMB2008)
    • Place of Presentation
      Toronto, Canada
    • Year and Date
      2008-07-21
    • Related Report
      2008 Annual Research Report
  • [Presentation] CAGE発現プロファイルを用いた転写開始点の発現パターンのクラスタリング手法2008

    • Author(s)
      寺家谷満, 瀬尾茂人, 竹中要一, 松田秀雄
    • Organizer
      日本分子生物学会第8回春季シンポジウム
    • Place of Presentation
      京王プラザホテル札幌
    • Year and Date
      2008-05-26
    • Related Report
      2009 Final Research Report
  • [Presentation] グラフ構造を用いた組織特異的な選択的スプライシングの解析手法2007

    • Author(s)
      瀬尾茂人, 竹中要一, 松田秀雄
    • Organizer
      日本分子生物学会第30回大会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-11
    • Related Report
      2009 Final Research Report 2007 Annual Research Report

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

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