Development of Gene Regulatory Network Analysis Methods for Revealing Cell Differentiation Processes

• Project/Area Number: 22310125
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: System genome science
• Research Institution: Osaka University
• Principal Investigator: MATSUDA Hideo 大阪大学, 情報科学研究科, 教授 (50183950)
• Co-Investigator(Kenkyū-buntansha): TAKENAKA Yoichi 大阪大学, 情報科学研究科, 准教授 (00324830)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥18,720,000 (Direct Cost: ¥14,400,000、Indirect Cost: ¥4,320,000); Fiscal Year 2012: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2011: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000); Fiscal Year 2010: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
• Keywords: 遺伝子ネットワーク / 細胞分化 / ベイジアンネットワーク / 遺伝子制御ネットワーク / 遺伝子発現プロファイル / バイオインフォマティクス / 遺伝子発現解析

Research Abstract

We constructed a mathematical model for expressing gene regulatory relationships, based on gene regulatory networks, on multiple cell differentiations. We successfully explored several regulatory genes appeared in both of the two cell differentiations of mouse adipocytes and osteoblasts. We developed a parallel processing method on massively parallel servers to reduce a large amount of computational costs of the processing.

Research Products

• [Journal Article] An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles (2013)
  • Author(s): Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: Gene Volume: Vol.518 Issue: 1 Pages: 17-25
  • DOI: 10.1016/j.gene.2012.11.090
  • Peer Reviewed
• [Journal Article] A Method for Isoform Prediction from RNA-Seq Data by Iterative Mapping (2012)
  • Author(s): Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: IPSJ Transactions on Bioinformatics Volume: 5 Issue: 0 Pages: 27-33
  • DOI: 10.2197/ipsjtbio.5.27
  • NAID: 130002124175
  • ISSN: 1882-6679
  • Peer Reviewed
• [Journal Article] An estimation method for inference of gene regulatory network using Bayesian network with uniting of partial problems (2012)
  • Author(s): Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: BMC Genomics Volume: Vol.13 Issue: Suppl 1 Pages: S12-S12
  • DOI: 10.1186/1471-2164-13-s1-s12
  • Peer Reviewed
• [Journal Article] Inference of S-system models of gene regulatory networks using immune algorithm (2011)
  • Author(s): Tomoyoshi Nakayama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: Journal of Bioinformatics and Computational Biology Volume: Vol.9 Issue: supp01 Pages: 75-86
  • DOI: 10.1142/s0219720011005768
  • Peer Reviewed
• [Journal Article] 細胞分化クロストークのモデル化と細胞分化クロストーク遺伝子の推定手法 (2011)
  • Author(s): 吉澤陽志, 瀬尾茂人, 竹中要一, 松田秀雄
  • Journal Title: 情報処理学会論文誌 数理モデル化と応用 Volume: 4巻 Pages: 59-68
  • NAID: 40019257169
  • Peer Reviewed
• [Journal Article] 細胞分化クロストークのモデル化と細胞分化クロストーク遺伝子の推定手法 (2011)
  • Author(s): 吉澤陽志
  • Journal Title: 情報処理学会論文誌数理モデル化と応用 Volume: Vol.4 Pages: 59-68
  • Peer Reviewed
• [Journal Article] Perfect Hamming code with a hash table for faster genome mapping (2011)
  • Author(s): Yoichi Takenaka
  • Journal Title: BMC Genomics Volume: Vol.12 Issue: Suppl 3 Pages: S8-S8
  • DOI: 10.1186/1471-2164-12-s3-s8
  • Peer Reviewed
• [Journal Article] Gene expression profile prospectively predicts peritoneal relapse after curative surgery of gastric cancer (2010)
  • Author(s): A.Takeno, I.Takemasa, S.Seno, M.Yamasaki, M.Motoori, H.Miyata, K.Nakajima, S.Takiguchi, Y.Fujiwara, T.Nishida, T.Okayama, K.Matsubara, Y.Takenaka, H.Matsuda, M.Monden, M.Mori, Y.Doki
  • Journal Title: Annals of Surgical Oncology Volume: Vol.17 Pages: 1033-1042
  • Peer Reviewed
• [Presentation] Estimate Dynamic Gene Regulatory Networks in Adipocyte Differentiation for Detecting Changes of Gene Regulations by Splitting Time Course Data (2012)
  • Author(s): Tomoyoshi Nakayama, Yoshiyuki Kido,Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: 23rd International Conference on Genome Informatics(GIW2012)
  • Place of Presentation: National Cheng Kung University, Tainan, Taiwan
  • Year and Date: 2012-12-13
• [Presentation] Large-Scale Gene Regulatory Network Analysis for Adipocyte Differentiation on High-Performance Computer (2012)
  • Author(s): Hideo Matsuda
  • Organizer: The 23rd International Conference on Genome Informatics (GIW2012)
  • Place of Presentation: National Cheng Kung University, Tainan, Taiwan
  • Year and Date: 2012-12-12
• [Presentation] スパコンによる遺伝子ネットワーク解析 (2012)
  • Author(s): 松田秀雄
  • Organizer: 電子情報通信学会2012年総合大会
  • Place of Presentation: 岡山大学(岡山県)
  • Year and Date: 2012-03-20
• [Presentation] Direct unique gene regulatory networks along dendrogram of cell differentiation (2011)
  • Author(s): Ryo Araki, Yoichi Takenaka, Tomoshige Ohno, Yukito Watanabe, Shigeto Seno, Hideo Matsuda
  • Organizer: InCoB/ISCB-Asia Joint Conference 2011
  • Place of Presentation: Renaissance Hotel, Kuala Lumpur, Malaysia
  • Year and Date: 2011-11-30
• [Presentation] Direct unique gene regulatory networks along dendrogram of cell differentiation (2011)
  • Author(s): Ryo Araki
  • Organizer: InCoB/ISCB-Asia Joint Conference 2011
  • Place of Presentation: ルネッサンスホテル(クアラルンプール、マレーシア)
  • Year and Date: 2011-11-30
• [Presentation] Network analysis for time-series expression profile using nested effects models (2011)
  • Author(s): Tatsuya Kitaguchi, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: The 2011 Joint Conference of CBI and JSBi (CBI/JSBi2011)
  • Place of Presentation: Kobe International Conference Center, Hyogo.
  • Year and Date: 2011-11-08
• [Presentation] Network analysis for time-series expression profile using nested effects models (2011)
  • Author(s): Tatsuya Kitaguchi
  • Organizer: Joint Conference of CBI and JSBi (CBI/JSBi2011)
  • Place of Presentation: 神戸国際会議場(兵庫県)
  • Year and Date: 2011-11-08
• [Presentation] A Directed Graphical Gaussian Model for Inferring Gene Regulatory Networks (2011)
  • Author(s): Tomoshige Ohno, Kiyoshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: The 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011)
  • Place of Presentation: Austria Center Vienna, Vienna, Austria
  • Year and Date: 2011-07-19
• [Presentation] A directed graphical Gaussian model for inferring gene regulatory networks (2011)
  • Author(s): Tomoshige Ohno
  • Organizer: Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011)
  • Place of Presentation: Austria Center Vienna(ウィーン、オーストリア)
  • Year and Date: 2011-07-19
• [Presentation] Feature selection for specifying experimental conditions that activate gene transcriptions (2011)
  • Author(s): Sho Ohsuga
  • Organizer: Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011)
  • Place of Presentation: Austria Center Vienna(ウィーン、オーストリア)
  • Year and Date: 2011-07-19
• [Presentation] A Method for Inference of Gene Regulatory Network based on Bayesian Network with Uniting of Partial Problems (2011)
  • Author(s): Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: The 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011)
  • Place of Presentation: Austria Center Vienna, Vienna, Austria.
  • Year and Date: 2011-07-18
• [Presentation] A method for inference of gene regulatory network based on Bayesian network with uniting of partial problems (2011)
  • Author(s): Yukito Watanabe
  • Organizer: Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011)
  • Place of Presentation: Austria Center Vienna(ウィーン、オーストリア)
  • Year and Date: 2011-07-18
• [Presentation] Revealing regulatory relationships of crosstalk with multiple time-series gene expression profiles (2010)
  • Author(s): Kiyoshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)
  • Place of Presentation: Centennial Hall, Kyushu University School of Medicine, Fukuoka.
  • Year and Date: 2010-12-13
• [Presentation] Revealing regulatory relationships of crosstalk with multiple time-series gene expression profiles (2010)
  • Author(s): K.Yoshizawa, S.Seno, Y.Takenaka, H.Matsuda
  • Organizer: Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)
  • Place of Presentation: 九州大学医学部百年講堂、福岡県
  • Year and Date: 2010-12-13
• [Presentation] Reconstruction of Gene Regulatory Networks for Drug Target Discovery (2010)
  • Author(s): Hideo Matsuda
  • Organizer: The 3rd National Seminar and Workshop on Computer Aided-Drug Design: Virtual Screening (CADD2010)
  • Place of Presentation: Gurney Hotel, Penang, Malaysia
  • Year and Date: 2010-12-03
• [Presentation] Reconstruction of gene regulatory networks for drug target discovery (2010)
  • Author(s): H.Matsuda
  • Organizer: 3rd Workshop on Computer Aided-Drug Design (CADD2010)
  • Place of Presentation: Gurney Hotel, Penang (Malaysia)(招待講演)
  • Year and Date: 2010-12-03
• [Presentation] 大規模遺伝子ネットワーク解析とその応用 (2010)
  • Author(s): 松田秀雄
  • Organizer: 情報計算化学生物学会2010年大会
  • Place of Presentation: 学術総合センター、東京都(招待講演)
  • Year and Date: 2010-09-15
• [Presentation] An estimation method of S-system model of gene regulatory networks using immune algorithm (2010)
  • Author(s): T.Nakayama, S.Seno, Y.Takenaka, H.Matsuda
  • Organizer: International Conference on Intelligent Sysmtes for Molecular Biology (ISMB2010)
  • Place of Presentation: Hynes Convention Center, Boston (USA)
  • Year and Date: 2010-07-12
• [Presentation] 時系列発現プロファイルのための遺伝子機能グループ解析手法
  • Author(s): 大熊祐太
  • Organizer: 情報処理学会バイオ情報学研究会
  • Place of Presentation: 沖縄科学技術大学院大学（沖縄県）
• [Presentation] Bayes-based inference of gene regulatory network for multiple time series gene expression profil
  • Author(s): Yukito Watanabe
  • Organizer: 生命医薬情報学連合大会
  • Place of Presentation: タワーホール船堀（東京都）
• [Presentation] Large-Scale Gene Regulatory Network Analysis for Adipocyte Differentiation on High-Performance Computer
  • Author(s): Hideo Matsuda
  • Organizer: International Conference on Genome Informatics (GIW2012)
  • Place of Presentation: National Cheng Kung University, Taiwan
  • Invited
• [Presentation] Estimate Dynamic Gene Regulatory Networks in Adipocyte Differentiation for Detecting Changes of Gene Regulations by Splitting Time Course Data
  • Author(s): Tomoyoshi Nakayama
  • Organizer: International Conference on Genome Informatics (GIW2012)
  • Place of Presentation: National Cheng Kung University, Taiwan