Statistical Analysis of causal relationship between the genes from gene expression data.

• Project/Area Number: 18681031
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: 基礎ゲノム科学
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: ABURATANI Sachiyo National Institute of Advanced Industrial Science and Technology, 生命情報工学研究センター, 研究員 (10361627)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥28,990,000 (Direct Cost: ¥22,300,000、Indirect Cost: ¥6,690,000); Fiscal Year 2008: ¥8,450,000 (Direct Cost: ¥6,500,000、Indirect Cost: ¥1,950,000); Fiscal Year 2007: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000); Fiscal Year 2006: ¥12,220,000 (Direct Cost: ¥9,400,000、Indirect Cost: ¥2,820,000)
• Keywords: 生体生命情報学 / マイクロアレイ / 発現制御 / 遺伝子ネットワーク / グラフィカル連鎖モデル / ウェブツール / 細胞周期 / 遺伝子発現 / ネットワーク推定 / 肝臓ガン進行過程 / 出芽酵母

Research Abstract

本研究では、発現プロファイルデータに既知の生物学的知見を加えて遺伝子間の因果性を推定する統計的手法を開発し、関連の有無や強弱に加え遺伝子間の因果性の解明を行った。また、開発した手法をウェブツールとして広く公開した。本研究で開発した手法は、数値データに既知の生物学的知見を加えた統計的手法であり、この手法を用いることによって、遺伝子間の発現相互作用について関連性の有無や強弱に加え遺伝子間の因果性の解明までを行うことが可能になった。

Research Products

• [Journal Article] Statistical Analysis of the Relationship between LexA-Regulated Genes from Expression Profiles (2008)
  • Author(s): Aburatani, S. and Horimoto, K.
  • Journal Title: Res. Commun. Biochem. Cell Mol. Biol. Vol.12, NOS.1&2 Pages: 119-135
  • Peer Reviewed
• [Journal Article] Integer Programming-based Approach to Allocation of Reporter Genes for Cell Array Analysis (2008)
  • Author(s): Hayashida, M., Sun, F., Aburatani, S., Horimoto, K. and Akutsu, T.
  • Journal Title: Int. J.Bioinformatics Research and Applications Vol.4(4) Pages: 385-399
  • NAID: 110006402728
  • Peer Reviewed
• [Journal Article] Network evaluation from the consistency of the graph structure with the measured data (2008)
  • Author(s): Saito, S., Aburatani, S. and Horimoto, K.
  • Journal Title: BMC Systems Biology Vol.2:84 Pages: 1-14
  • Peer Reviewed
• [Journal Article] Network evaluation from the consistency of the graph structure with the measured data (2008)
  • Author(s): Saito, S., Aburatani, S., Horimoto, K.
  • Journal Title: BMC Systems Biology Vol.2:84 Pages: 1-14
  • Peer Reviewed
• [Journal Article] Integer Programming-based Approach to Allocation of Reporter Genes for Cell Array Analysis (2008)
  • Author(s): Hayashida, M., Sun, F., Aburatani, S., Horimoto, K., Akutsu, T.
  • Journal Title: Int.J.Bioinformatics Research and Applications, Vol.4(4) Pages: 385-399
  • NAID: 110006402728
  • Peer Reviewed
• [Journal Article] Statistical Analysis of the Relationship between LexA-Regulated Genes from Expression Profiles (2008)
  • Author(s): Aburatani, S., Horimoto, K.
  • Journal Title: Res.Commun.Biochem.Cell Mol.Biol. Vol.12 NOS.1&2 Pages: 119-135
  • Peer Reviewed
• [Journal Article] Gene systems network inferred from expression profiles in hepatocellular carcinogenesis by graphical Gaussian model (2007)
  • Author(s): Aburatani, S., Sun, F., Saito, S., Honda, M., Kaneko, S. and Horimoto, K.
  • Journal Title: EURASIP J. Bioinfo. Systems Biol. Vol.47214 Pages: 1-11
  • Peer Reviewed
• [Journal Article] Integer Programming-based Approach to Allocation of Reporter Genes for Cell Array Analysis (2007)
  • Author(s): Hayashida, M., Sun, F., Aburatani, S., Horimoto, K. and Akutsu, T.
  • Journal Title: Proceedings of OSB2007 Pages: 21-28
  • NAID: 110006402728
  • Peer Reviewed
• [Journal Article] ASIAN : A Network Inference Web Server for Biologists (2007)
  • Author(s): Aburatani, S.
  • Journal Title: Proceedings of the 11th World Multiconference on Systemics, Cybernetics and Informatics Vol.4 Pages: 1-6
  • Peer Reviewed
• [Journal Article] Inference of Complex Regulatory Network for the Cell Cycle System in Saccharomyces cerevisiae (2007)
  • Author(s): Aburatani, S.
  • Journal Title: Algebraic Biology 2007 Lecture Notes in Computer Science Pages: 350-364
• [Journal Article] nteger Programming-based Approach to Allocation of Reporter Genes for Cell Attsy Analysis (2007)
  • Author(s): Hayashida, M., Sun, F., Aburatani, S., Horimoto, K. and Akutsu, T
  • Journal Title: JBRA (In press)
  • Peer Reviewed
• [Journal Article] ASIAN: A Network Inference Web Sever for Biologists (2007)
  • Author(s): Aburatani, S.
  • Journal Title: Proceedings of the 11th World Multiconference on Systemics, Cybernetics and Informatics 4 Pages: 1-6
  • Peer Reviewed
• [Journal Article] Interger Programming-based Approach to Allocation of Reporter Genes for Cell Array Analysis (2007)
  • Author(s): Hayashida, M., Sun, F., Aburatani S., Horimoto, K. and Akutsu, T.
  • Journal Title: Proceedings of 10th OSB, Lecture Notes in Operation Research Pages: 18-21
  • Peer Reviewed
• [Journal Article] Inference of Complex Regulatory Network for the Cell Cycle System in Saccharomtces cerevisiae (2007)
  • Author(s): Aburatani, S.
  • Journal Title: Proceedings of the Algebraic Biology 2007 4545 Pages: 350-364
  • Peer Reviewed
• [Journal Article] Gene systems network inferred from expression profikes in he patocellular carcinogenesis by graphical Gaussian model (2007)
  • Author(s): Aburatani, S., Sun, F., Saito, S., Honda, M., Kaneko, S.and Horimoto, K.
  • Journal Title: EURASIP Journal on Bioinformatics and Systems Biology Pages: 47214-47225
  • Peer Reviewed
• [Journal Article] Inference of Complex Regulatory Network for the Cell Cycle System in Saccharomyces cerevisiae (2007)
  • Author(s): Aburatani, S.
  • Journal Title: Proceedings of the Algebraic Biology 2007 (in press)
• [Journal Article] A Graphical Chain Modeling Approach for Analyzing Gene Expression Profiles (2006)
  • Author(s): Aburatani, S., Saito, S., Toh, H., Horimoto, K.
  • Journal Title: Statist. Method. Vol.3 Pages: 17-28
  • NAID: 110003482758
  • Peer Reviewed
• [Journal Article] Serial Network Inference in Cell Cycle regulation on Yeast (2006)
  • Author(s): Aburatani, S. and Horimoto, K.
  • Journal Title: Proceedings of the 10th World Multiconference on Systemics, Cybernetics and Informatics Vol.4 Pages: 1-6
  • Peer Reviewed
• [Journal Article] Serial Network Inference in Cell Cycle regulation on Yeast (2006)
  • Author(s): Aburatani, S., Horimoto, K.
  • Journal Title: Proceedings of the 10th World Multiconference on Systemics, Cybernetics and Informatics 4 Pages: 1-6
• [Journal Article] A Graphical Chain Modeling Approach for Analyzing Gene Expression Profiles (2006)
  • Author(s): Aburatani, S., Saito, S., Toh, H., Horimoto, K.
  • Journal Title: Statist. Method. 3 Pages: 17-28
  • NAID: 110003482758
• [Journal Article] Gene systems network inferred from expression profiles in hepatocellular carcinogenesis by graphical Gaussian model
  • Author(s): Aburatani, S., Sun, F., Saito, S., Honda, M., Kaneko, S., Horimoto, K.
  • Journal Title: EURASIP Journal on Bioinformatics and Systems Biology (accepted)
• [Presentation] Inference of Complex Regulatory Network for the Cell Cycle System in Saccharomyces cerevisiae (2007)
  • Author(s): Aburatani, S.
  • Organizer: Algebraic Biology 2007
  • Place of Presentation: RISC (Austria)
• [Presentation] ASIAN ; A Network Inference Web Server for Biologists (2007)
  • Author(s): Aburatani, S.
  • Organizer: WMSCI2007
  • Place of Presentation: Orland (USA)
• [Presentation] Serial Network Inference in Cell Cycle Regulation on Yeast (2006)
  • Author(s): Aburatani, S.
  • Organizer: Horimoto, K., WMSCI2006
  • Place of Presentation: Orland (USA)
• [Presentation] Inference of Cell Cycle Regulatory Network from Expression Profiles by Graphical Chain Modeling (2006)
  • Author(s): Aburatani, S., Saito, S., Horimoto, K.
  • Organizer: 20th IUBMB International Congress of Biochemistry and Molecular Biology
  • Place of Presentation: Kyoto (Japan)
• [Book] Bioinformatics for Systems Biology : Chapter 29 : ASIAN : Network Inference Web Server (Stephen Krawetz 編集, 2009.2) (2009)
  • Author(s): Aburatani, S., Saito, S., Horimoto, K.
  • Total Pages: 740
  • Publisher: Humana Press
• [Book] Bioinformatics for Systems Biology Chapter 29 : ASIAN : Network Inference Web Server, (2009)
  • Author(s): S.Aburatani, S.Saito, K.Horimoto
  • Publisher: Humana Press
• [Book] マイクロアレイデータ統計解析プロトコール : 偏相関係数によるネットワーク推定グラフィカル・ガウシアン・モデル法", (藤渕航・堀本勝久 / 編, pp.224-233, 2008.4) (2008)
  • Author(s): 油谷幸代
  • Total Pages: 255
  • Publisher: 羊土社
• [Book] マイクロアレイデータ統計解析プロトコール(実験医学別冊23)4章ネットワーク解析[応用解析編]1.偏相関係数によるネットワーク推定グラフィカル・ガウシアン・モデル法, (2008)
  • Author(s): 油谷幸代 (藤渕航, 堀本勝久編)
  • Publisher: 羊土社
• [Book] Bioinformatics for Systems Biology: Srcond Edition, Introduction to Informattics (2008)
  • Author(s): Aburatani, S., Saito, S., and Horimoto,K.
  • Publisher: The Humana Press, New Jersey, in press
• [Book] はじめてのバイオインフォマティクス : トランスクリプトームとプロテオーム (籐博幸 編集, pp97-123, 2006.12) (2006)
  • Author(s): 油谷幸代
  • Total Pages: 166
  • Publisher: 講談社サイエンティフィック
• [Remarks] ASIAN : 階層クラスタリングとグラフィカル・ガウシアン・モデリング(GGM)の組み合わせによるネットワーク推定ツール
  • URL: http://eureka.cbrc.jp/asian/
• [Remarks] LB001 ASIAN : 階層クラスタリングとグラフィカル・ガウシアン・モデリング(GGM)の組み合わせによるネットワーク推定ツール
  • URL: http://eureka.cbrc.jp/asian/