Systems evolutionary analysis on Hox transcription networks in the early embryonic development

• Project/Area Number: 20700266
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: Tokyo Medical and Dental University
• Principal Investigator: OGISHIMA Soichi Tokyo Medical and Dental University, 難治疾患研究所, 助教 (40447496)
• Project Period (FY): 2008 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000); Fiscal Year 2009: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2008: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
• Keywords: システム生物 / システム進化 / 初期胚発生 / Hox / 生命情報学

Research Abstract

We identified Hox transcriptional networks which have key roles in regulating the patterning of the antero-posterior axis at phylotypic stage in a metazoan embryo. We conducted bioinformatics methods including promoter analysis on Hox regulating genes in each evolutionary stage and anatomical structure which were retrieved from public gene expression database. We then compared Hox transcriptional networks among mouse, sea squirt, and fruit fly.

Research Products

• [Journal Article] Combined in silico and in vivo analyses reveal role of Hes1 in taste cell differentiation. (2009)
  • Author(s): Ota MS, Kaneko Y, Kondo K, Ogishima S, Tanaka H, Eto K, Kondo T
  • Journal Title: PLoS Genetics 5(4)
  • Peer Reviewed
• [Journal Article] BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network. (2009)
  • Author(s): Ishiwata RR, Morioka MS, Ogishima S†, Tanaka H
  • Journal Title: Bioinformatics 25(4) Pages: 543-4
• [Journal Article] Combined in silico and in vivo analyses reveal role of Hes1 in taste cell differentiation (2009)
  • Author(s): Ota, MS., Kaneko, Y., Kondo, K., Ogishima, S., Tanaka, H., Eto, K., Kondo, T.
  • Journal Title: PLoS Genetics 5
  • Peer Reviewed
• [Journal Article] BioCichlid : central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network. (2009)
  • Author(s): Ryosuke R Ishiwata, Masaki S Morioka, Soichi Ogishima, Hiroshi Tanaka
  • Journal Title: Bioinformatics 25 Pages: 543-544
  • Peer Reviewed
• [Presentation] Preliminary analysis on systems evolution of the putative Hox transcriptional network (2009)
  • Author(s): Soichi Ogishima, Hiroshi Tanaka
  • Organizer: OWECS 2009
  • Place of Presentation: OIST(Okinawa, Japan)
  • Year and Date: 2009-12-08
• [Presentation] 酵母タンパク質問相互作用ネットワークにおける機能モジュールの進化的拘束 (2009)
  • Author(s): 菊地正隆, 荻島創一, 新村芳人, 田中博
  • Organizer: 日本進化学会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2009-09-03
• [Presentation] Systems evolutionary analysis on the putative Hox transcriptional networks. (2009)
  • Author(s): Ogishima S, Tanaka H
  • Organizer: European Society for Evolutionary Biology 2009
  • Place of Presentation: Politecnico di Torino, Italy
  • Year and Date: 2009-08-25
• [Presentation] Systems evolutionary analysis on the putative Hox transcriptional networks (2009)
  • Author(s): Soichi Ogishima, Hiroshi Tanaka
  • Organizer: European Society for Evolutionary Biology 2009
  • Place of Presentation: Politecnico di Torino(Italy)
  • Year and Date: 2009-08-25
• [Presentation] Preliminary analysis on systems evolution of the putative Hox transcriptional network. (2009)
  • Author(s): Ogishima S, Tanaka H
  • Organizer: OWECS 2009
  • Place of Presentation: OIST, Okinawa
  • Year and Date: 2009-08-08
• [Presentation] Preliminary analysis on systems constraints in the putative Hox transcriptional network. (2008)
  • Author(s): Ogishima S, Tanaka H
  • Organizer: 2nd meeting of Euro EvoDevo
  • Place of Presentation: Ghent University, Belgium
  • Year and Date: 2008-07-31
• [Presentation] Preliminary analysis on systems constraints in the putative Hox transcriptional network. (2008)
  • Author(s): Soichi Ogishima, Hiroshi Tanaka
  • Organizer: 2nd meeting of Euro EvoDevo
  • Place of Presentation: Ghent University (Belgium)
  • Year and Date: 2008-07-31
• [Presentation] Systems biology and evolution: toward understanding of the grand design of biological systems. (2008)
  • Author(s): Ogishima S, Tanaka H
  • Organizer: Bioinformatik-Kolloquium
  • Place of Presentation: Goettingen University, Germany
  • Year and Date: 2008-07-14
• [Presentation] Systems biology and evolution : toward understanding of the grand design of biological systems. (2008)
  • Author(s): Soichi Ogishima, Hiroshi Tanaka
  • Organizer: Bioinformatik-Kolloquium
  • Place of Presentation: Goettingen University (Gemany)
  • Year and Date: 2008-07-14
• [Presentation] Systems biology and evolution: toward understanding of the grand design of biological systems. (2008)
  • Author(s): Ogishima S, Tanaka H
  • Organizer: BIOQUANT iBioS Meeting
  • Place of Presentation: Heidelberg University, Germany
  • Year and Date: 2008-05-27
• [Presentation] Systems biology and evolution : toward understanding of the grand design of biological systems. (2008)
  • Author(s): Soichi Ogishima, Hiroshi Tanaka
  • Organizer: BIOQUANT iBioS Meeting
  • Place of Presentation: Heidelberg University (Gemany)
  • Year and Date: 2008-05-27
• [Book] オープンソースで学ぶバイオインフォマティクス (2008)
  • Author(s): オープンバイオ研究会(編), 片山俊明, 荒川和晴, 二階堂愛, 荻島創一, 田中伸也, 中尾光輝
  • Publisher: 東京電機大学出版局
• [Book] マイクロアレイデータ統計解析プロトコール (2008)
  • Author(s): 藤渕航(編), 堀本勝久(編), 荻島創一, ほか
  • Publisher: 羊土社