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2007 Fiscal Year Annual Research Report

ゲノム機能解析とインフォマティクスを駆使した生命システムの解明

Research Project

Project/Area Number 16063101
Research InstitutionThe University of Tokyo

Principal Investigator

高木 利久  The University of Tokyo, 大学院・新領域創成科学研究科, 教授 (30110836)

Co-Investigator(Kenkyū-buntansha) 小笠原 直毅  奈良先端科学技術大学院大学, 情報科学研究科, 教授 (10110553)
藤山 秋佐夫  国立情報学研究所, 情報学プリンシプル研究系, 教授 (60142311)
辻 省次  東京大学, 医学部附属病院, 教授 (70150612)
小原 雄治  国立遺伝学研究所, 生物遺伝資源情報総合センター, 教授 (70135292)
菅野 純夫  東京大学, 大学院・新領域創成科学研究科, 教授 (60162848)
Keywords生命システム / ゲノム機能解析 / 生命シミュレーション / バイオインフォマティクス / 遺伝子ネットワーク / 表現型解析 / ゲノムオントロジー / システム生物学
Research Abstract

本総括班は、「ゲノム機能解析とインフォマティクスを駆使した生命システムの解明」(略称:生命システム情報)を有機的かつ円滑に運営し、研究を効率良く進めるためのものである。また、この総括班は、「生命システム情報」だけでなく、「比較ゲノム」、「応用ゲノム」、「基盤ゲノム」を含む、ゲノム特定4領域全体の総括班としての機能も果たすように設計されている。そのため、ゲノム特定4領域の有機的、効率的運営のための活動もあわせて展開する。また、国内の関連プロジェクトやセンターとの連絡調整機能も果たす。
平成19年度に行ったおもな活動は以下の通りである。
・ゲノム特定4領域の計画研究(66課題)、公募研究(103課題)、支援班(5課題)の班員による合同班会議(平成19年6月25日〜27日、神戸)の開催
・ゲノム研究者と一般市民の交流イベント「ゲノムひろば」(平成19年10月13日〜14日大阪)の開催
・領域横断微生物研究会(平成19年9月23日〜25日、広島)の開催
・インフォマティクス研究者と医学研究者の交流会(平成19年11月22日〜23日、柏)の開催
・高校生をおもな対象とした、研究者と市民との交流会「ミニゲノムひろば」(平成19年12月23日、福岡)の開催
・成果公開シンポジウム(平成20年1月28日、東京)の開催
・ホームページの運用、市民向け解説記事の充実、英語ページの作成
・ゲノム特定4領域の電子名簿および平成19年度研究成果報告書の作成
・ゲノム特定4領域で開発されたデータベースなどの成果公開用サーバの整備
・班員専用SNS(ソーシャルネットワーキングサービス)システム開設

  • Research Products

    (43 results)

All 2008 2007 Other

All Journal Article (27 results) (of which Peer Reviewed: 27 results) Presentation (6 results) Book (6 results) Remarks (4 results)

  • [Journal Article] The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants.2008

    • Author(s)
      Rensing, S, A. (Fujiyama, A., Kohara, Y., Sugano, S.)
    • Journal Title

      Science 319(5859)

      Pages: 64-69

    • Peer Reviewed
  • [Journal Article] Familial cases presenting very early onset autosomal dominant Alzheimer's disease with I143T in presenilin-1 gene: Implication for genotype-phenotype correlation.2008

    • Author(s)
      Arai, N. (Tsuji, S.)
    • Journal Title

      Neurogenetics (印刷中)

    • Peer Reviewed
  • [Journal Article] Development of high-throughput microarray-based resequencing system for neurological disorders and its application to molecular genetics of amyotrophic lateral sclerosis.2008

    • Author(s)
      Takahashi, Y. (Tsuji, S.)
    • Journal Title

      Arch Neurol. (印刷中)

    • Peer Reviewed
  • [Journal Article] Total deletion and a missense mutation of ITPR1 in Japanese SCA15 families.2008

    • Author(s)
      Hara, K. (Tsuji, S.)
    • Journal Title

      Neurol. (印刷中)

    • Peer Reviewed
  • [Journal Article] Discrimination between stable and dynamic components of proteincomplexes by means of quantitative proteomics.2008

    • Author(s)
      Kito, K. (Ito, T.)
    • Journal Title

      Proteomics (印刷中)

    • Peer Reviewed
  • [Journal Article] DBTSS:database of transcription start sites, progress report 2008.2008

    • Author(s)
      Wakaguri, H. (Sugano, S.)
    • Journal Title

      Nucleic Acids Res. 36

      Pages: 97-100

    • Peer Reviewed
  • [Journal Article] Reconstruction of highly heterogeneous gene-content evolution across the three domains of life2007

    • Author(s)
      Iwasaki, W. (Takagi, T.)
    • Journal Title

      Bioinformatics 23(13)

      Pages: 230-239

    • Peer Reviewed
  • [Journal Article] OReFiL: an online resource finder for life sciences2007

    • Author(s)
      Yamamoto, Y. (Takagi, T.)
    • Journal Title

      BMC Bioinformatics 8

      Pages: 287

    • Peer Reviewed
  • [Journal Article] Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes2007

    • Author(s)
      Kurokawa, K. (Takagi, T.)
    • Journal Title

      DNA Research 14(4)

      Pages: 169-181

    • Peer Reviewed
  • [Journal Article] Intrinsic promoter activities of primary DNA sequences in the human genome2007

    • Author(s)
      Sakakibara, Y. (Takagi, T.)
    • Journal Title

      DNA Research 14(2)

      Pages: 71-77

    • Peer Reviewed
  • [Journal Article] Biomedical knowledge navigation by literature clustering2007

    • Author(s)
      Yamamoto, Y. (Takagi, T.)
    • Journal Title

      Journal of Biomedical Informatics 40(2)

      Pages: 114-130

    • Peer Reviewed
  • [Journal Article] Knowledge discovery based on an implicit and explicit conceptual network2007

    • Author(s)
      Koike, A. (Takagi, T.)
    • Journal Title

      Journal of the American Society for Information Science and Technology 58(1)

      Pages: 51-65

    • Peer Reviewed
  • [Journal Article] The medaka draft genome and insights into vertebrate genome evolution.2007

    • Author(s)
      Kasahara, M. (Fujiyama, A., Kohara, Y.)
    • Journal Title

      Nature 447

      Pages: 714-719

    • Peer Reviewed
  • [Journal Article] UTGB/medaka: genomic resource database for medaka biology.2007

    • Author(s)
      Ahsan, B. (Fujiyama, A.)
    • Journal Title

      Nucleic Acids Res. (印刷中)

    • Peer Reviewed
  • [Journal Article] Sox9b/sox9a2-EGFP transgenic medaka reveals the morphological reorganization of the gonads and a common precursor of both the female and male supporting cells.2007

    • Author(s)
      Nakamura, S. (Fujiyama, A.)
    • Journal Title

      Mol Reprod Dev. (印刷中)

    • Peer Reviewed
  • [Journal Article] Asian Origin for the Worldwide-Spread Mutational Event in Machado-Joseph Disease.2007

    • Author(s)
      Martins, S. (Tsuji, S.)
    • Journal Title

      Arch Neurol. Oct;64(10)

      Pages: 1502-1508

    • Peer Reviewed
  • [Journal Article] Retrotransposon Silencing by DNA Methylation can Drive Mammalian Genomic Imprinting.2007

    • Author(s)
      Suzuki, S. (Kohara, Y.)
    • Journal Title

      PLos Genetics 3,No.4

      Pages: 55

    • Peer Reviewed
  • [Journal Article] RUNX regulates stem cell proliferation and differentiation: Insights from studies of C. elegans.2007

    • Author(s)
      Kagoshima, H. (Kohara, Y.)
    • Journal Title

      J Cell Biochem. Apr 1;100(5)

      Pages: 1119-1130

    • Peer Reviewed
  • [Journal Article] The C. elegans CBFb homologue BRO-1 interacts with the Runx factor, RNT-1, to promote stem cell proliferation and self-renewal.2007

    • Author(s)
      Kagoshima, H.(Kohara, Y.)
    • Journal Title

      Development 134

      Pages: 3905-3915

    • Peer Reviewed
  • [Journal Article] Proteomic analysis of in vivo 14-3-3 interactions in the yeast Saccharomyces cerevisiae.2007

    • Author(s)
      Kakiuchi, K. (Ito, T.)
    • Journal Title

      Biochemistry 46

      Pages: 7781-7792

    • Peer Reviewed
  • [Journal Article] Structure and function of the PB1 domain, a protein interactionmodule conserved in animals, fungi, amoebas, and plants.2007

    • Author(s)
      Sumimoto, H.(Ito, T.)
    • Journal Title

      Science's STKE 007

      Pages: 6

    • Peer Reviewed
  • [Journal Article] Distribution of stable DnaA-binding sites on the Bacillus subtilisgenome Detected using a modified ChIP-chip method.2007

    • Author(s)
      Ishikawa, S. (Ogasawara, N.)
    • Journal Title

      DNA Res. 14

      Pages: 155-168

    • Peer Reviewed
  • [Journal Article] The entire organization of transcription units on the Bacillus subtilis genome.2007

    • Author(s)
      Kobayashi, H. (Ogasawara, N.)
    • Journal Title

      BMC Genomics 8

      Pages: 197

    • Peer Reviewed
  • [Journal Article] Isolation and characterization of a dominant negative mutant of Bacillus subtilis GTP-binding Protein, YlqF, essential for biogenesis and maintenance of the 50S ribosomal subunit.2007

    • Author(s)
      Matsuo, Y. (Ogasawara, N.)
    • Journal Title

      J Biol Chem. 282

      Pages: 25270-25277

    • Peer Reviewed
  • [Journal Article] Functional gene screening system identified TRPV4 as a regulator of chondrogenic differentiation.2007

    • Author(s)
      Muramatsu, S. (Sugano, S.)
    • Journal Title

      J Biol Chem. 282

      Pages: 32158-32167

    • Peer Reviewed
  • [Journal Article] Distinct class of putative "non-conserved"promoters in humans: Comparative studies of alternative promoters of human and mouse genes.2007

    • Author(s)
      Tsuritani, K. (Sugano, S.)
    • Journal Title

      Genome Res. 17

      Pages: 1005-1014

    • Peer Reviewed
  • [Journal Article] Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome.2007

    • Author(s)
      Sakakibara, Y.(Sugano, S.)
    • Journal Title

      DNA Res. 14

      Pages: 71-77

    • Peer Reviewed
  • [Presentation] Unexpected complexity of the budding yeast transcriptome: Yeast as a potential model organism for ncRNA research.2007

    • Author(s)
      Ito, T.
    • Organizer
      The 7th International Workshop on Advanced Genomics
    • Place of Presentation
      Tokyo
    • Year and Date
      2007-11-28
  • [Presentation] デュアルベイト逆2ハイブリッドシステムとPCS-MSによるタンパク質間相互作用の機能解析2007

    • Author(s)
      伊藤隆司
    • Organizer
      日本ヒトプロテオーム機構第5回大会
    • Place of Presentation
      東京
    • Year and Date
      2007-07-30
  • [Presentation] Distribution of Transcription Elongatio Factor NusA and GreA in Bacillus subtilis.2007

    • Author(s)
      Kusuya, Y.(Ogasawara, N.)
    • Organizer
      4th Conference on Functional. Genomics of Gram-Positive Microorganisms
    • Place of Presentation
      Pisa, Italy.
    • Year and Date
      2007-06-25
  • [Presentation] Regulation of initiation of replication of the Bacillus subtilis genomeby DnaA and YabA.2007

    • Author(s)
      Cho, E.(Ogasawara, N.)
    • Organizer
      4th Conference on Functional Genomics of Gram-Positive Microorganisms
    • Place of Presentation
      Pisa, Italy.
    • Year and Date
      2007-06-25
  • [Presentation] In vivo dynamics of the Bacillus subtilis RNA polymerase on the Genome.2007

    • Author(s)
      Ishikawa, S.(Ogasawara, N.)
    • Organizer
      4th Conference on Functional Genomics of Gram-Positive Microorganisms
    • Place of Presentation
      Pisa, Italy.
    • Year and Date
      2007-06-24
  • [Presentation] Y2H and MS approaches for annotating protein interactions and modifications, Interactome Mapping Project for Human and Model Organisms.2007

    • Author(s)
      Ito, T.
    • Organizer
      Cold Spring Harbor
    • Place of Presentation
      NY, USA
    • Year and Date
      2007-04-24
  • [Book] 医学生物学分野におけるシソーラスとテキストマイニング技術の開発(実験医学増刊号Vol.26, No.7)2008

    • Author(s)
      小池麻子(高木利久)
    • Total Pages
      6
    • Publisher
      羊土社
  • [Book] The Five Year Project for Genome Research in Japan: Genome Science 2004-2009(special issue, Bioinformatics in Japnan, (2007)11, 1030-1032)2007

    • Author(s)
      Fujiyama, A
    • Total Pages
      3
    • Publisher
      Asia Pacific Biotech News
  • [Book] ヒトへの進化のゲノム基盤、ヒト・霊長類の比較ゲノム解析(「実験医学」25, 226-231)2007

    • Author(s)
      渡邉日出海(藤山秋佐夫)
    • Total Pages
      6
    • Publisher
      羊土社
  • [Book] ヒトーチンプY染色体の常染色体よりも早い進化male-driven evolutionの可能性(「遺伝 別冊」No.20, 138-143)2007

    • Author(s)
      黒木陽子(藤山秋佐夫)
    • Total Pages
      6
    • Publisher
      裳華房
  • [Book] ヒトと霊長類の比較ゲノム:近縁種との比較から見るヒトゲノムの特徴(「細胞工学別冊 比較ゲノム学から読み解く生命システム」pp43-49)2007

    • Author(s)
      黒木陽子(藤山秋佐夫)
    • Total Pages
      7
    • Publisher
      秀潤社
  • [Book] Chapter 9 Methods for protein-protein interaction analysis (「Introduction to Systems Biology」542, pp160-182)2007

    • Author(s)
      Kito, K.(Ito, T)
    • Total Pages
      23
    • Publisher
      Humana Press
  • [Remarks] Takagi, T. BioTermNet:明示的/潜在的な概念間の関係性のネットワークの可視化

    • URL

      http://btn.ontology.ims.u-tokyo.ac.jp/

  • [Remarks] Takagi, T. OReFiL:インターネット上のデータベースやツールなどの検索システム

    • URL

      http://orefil.dbcls.jp/

  • [Remarks] Ito, T.出芽酵母完全長cDNA解析プロジェクトホームページ

    • URL

      http://itolab.cb.k.u-tokyo.ac.jp/GCap/

  • [Remarks] Ito, T. UT Genome Browser for yeast

    • URL

      http://yeast.utgenome.org/

URL: 

Published: 2010-02-04   Modified: 2014-12-10  

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