A method for exhaustive similarity search of genomic positional expression.

• Project/Area Number: 19700275
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: Osaka 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: ¥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.

Research Products

• [Journal Article] Improved prediction method for protein interactions using both structural and functional characteristics of proteins (2010)
  • Author(s): Tatsuya Yoshikawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: IPSJ Transactions on Bioinformatics vol.3 Pages: 10-23
  • Peer Reviewed
• [Journal Article] Improved prediction method for protein interactions using both structural and functional characteristics of proteins (2010)
  • Author(s): Tatsuya Yoshikawa
  • Journal Title: IPSJ Transactions on Bioinformatics 3 Pages: 10-23
  • Peer Reviewed
• [Journal Article] A Combination Method of the Tanimoto Coefficient and Proximity Measure of Random Forest for Compound Activity Prediction (2008)
  • Author(s): Gen Kawamura, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: IPSJ Transactions on Bioinformatics Vol.49No.SIG5 Pages: 46-57
  • NAID: 110006824830
• [Journal Article] A Distributed-Processing System for Accelerating Biological Research using Data-Staging (2008)
  • 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
• [Journal Article] A Distributed-Processing System for Accelerating Biological Research using -Staging
  • Author(s): Yoshiyuki Kido
  • Journal Title: IPSJ Transactions on Bioinformatics In press
  • 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
  • Peer Reviewed
• [Presentation] An approach for efficient computational analysis of massive RNA-Seq data (2009)
  • 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
• [Presentation] An approach for efficient computational analysis of massive RNA-Sea data (2009)
  • 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
• [Presentation] A method for analyzing gene expression profiles based on the underlying structures (2009)
  • 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
• [Presentation] A method for analysis of tissue-specific alternative transcripts using CAGE tags (2008)
  • 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
• [Presentation] A Clustering Method for Expression Patterns of Transcription Starting Sites (2008)
  • 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
• [Presentation] A method for analysis of tissue-specific alternative transcripts using CAGE tags (2008)
  • Author(s): Shigeto Seno
  • Organizer: Intelligent Systems for Molecular Biology(ISMB2008)
  • Place of Presentation: Toronto, Canada
  • Year and Date: 2008-07-21
• [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
• [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