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2010 Fiscal Year Final Research Report

Interaction map to elucidate structural transformations in biological systems

Research Project

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Project/Area Number 17017006
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo

Principal Investigator

ARITA Masanori  The University of Tokyo, 大学院・理学系研究科, 准教授 (10356389)

Project Period (FY) 2005 – 2010
Keywords代謝 / データベース / フラボノイド / バイオポータル
Research Abstract

A portal site was created to host chemical information on basic metabolites, lipid, plant secondary metabolites (flavonoids), scientific classification of plant species, and crude drug and Kampo information. The site functions as an integrative portal for metabolomics by including information on biochemical reactions, metabolic pathways, literature, and academic societies. The same system is used by a few domestic societies to achieve a cross-societal network.

  • Research Products

    (48 results)

All 2011 2010 2009 2008 2007 2006 2005 Other

All Journal Article (17 results) (of which Peer Reviewed: 17 results) Presentation (15 results) Book (11 results) Remarks (5 results)

  • [Journal Article] Reconstructing phylogeny from metabolic substrate-product relationships2011

    • Author(s)
      Chang CW, Lyu PC, Arita M
    • Journal Title

      BMC Bioinformatics (Proceedings 9th APBC in Korea) 12(Suppl 1)

      Pages: S27

    • Peer Reviewed
  • [Journal Article] Nested structure acquired through simple evolutionary process2010

    • Author(s)
      Takemoto K, Arita M
    • Journal Title

      Journal of Theoretical Biology 264(3)

      Pages: 782-786

    • Peer Reviewed
  • [Journal Article] Bistable stochastic processes in the q-exponential family2010

    • Author(s)
      Hasegawa Y, Arita M
    • Journal Title

      Physica A 389(21)

      Pages: 4450-4461

    • Peer Reviewed
  • [Journal Article] A pitfall of wiki solution for biological databases2009

    • Author(s)
      Arita M
    • Journal Title

      Briefings Bioinformatics 10(3)

      Pages: 295-296

    • Peer Reviewed
  • [Journal Article] Heterogeneous distribution of metabolites across plant species2009

    • Author(s)
      Takemoto K, Arita M
    • Journal Title

      Physica A 388(13)

      Pages: 2771-2780

    • Peer Reviewed
  • [Journal Article] Traceable analysis of multiple-stage mass spectra through precursor-product annotations2009

    • Author(s)
      Horai H, Arita M, Ojima Y, Nihei Y, Kanaya S, Nishioka T
    • Journal Title

      Proceedings of German Conference in Bioinformatics (GCB'09) (GI-Edition Lecture Notes in Informatics), Halle, Germany 157

      Pages: 173-178

    • Peer Reviewed
  • [Journal Article] Ontology checking and integration of crude-drug and kampo information2009

    • Author(s)
      Arita M, Suwa K, Yoshimoto M, Hirai A, Kanaya S
    • Journal Title

      Proceedings of the 2nd International Conference of Biomedical Engineering and Informatics (BMEI2009), Tianjin China 3

      Pages: 1304-1307

    • Peer Reviewed
  • [Journal Article] Properties of the maximum q-likelihood estimator for independent random variables2009

    • Author(s)
      Hasegawa Y, Arita M
    • Journal Title

      Physica A 388

      Pages: 3399-3412

    • Peer Reviewed
  • [Journal Article] Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach2009

    • Author(s)
      Fukushima A, Kanaya S, Arita M
    • Journal Title

      Plant Biotechnology 26

      Pages: 485-493

    • Peer Reviewed
  • [Journal Article] Period-phase map : two-dimensional selection of circadian rhythm-related genes2009

    • Author(s)
      Morioka R, Arita M, Sakamoto K, Kawaguchi S, Tei H, Horimoto K
    • Journal Title

      IET System Biology 3(6)

      Pages: 487-495

    • Peer Reviewed
  • [Journal Article] Time-resolved metabolomics reveals metabolic modulation in rice foliage2008

    • Author(s)
      Sato S, Arita M M, Soga T, Nishioka T, Tomita M
    • Journal Title

      BMC Systems Biology 2

      Pages: 51

    • Peer Reviewed
  • [Journal Article] Search extension transforms Wiki into a relational system : a case for flavonoid metabolite database2008

    • Author(s)
      Arita M, Suwa K
    • Journal Title

      BMC BioData Mining 1

      Pages: 7

    • Peer Reviewed
  • [Journal Article] SVD-based anatomy of gene-expression for correlation analysis in Arabidopsis thaliana2008

    • Author(s)
      Fukushima A, Wada M, Kanaya S, Arita M
    • Journal Title

      DNA research 15(6)

      Pages: 367-374

    • Peer Reviewed
  • [Journal Article] Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions2007

    • Author(s)
      Okada K, Asai K, Arita M
    • Journal Title

      Proceedings of 5th Asia Pacific Bioinformatics Conference (APBC2007), Hong Kong

    • Peer Reviewed
  • [Journal Article] Detection of monosaccharide types from coordinates2007

    • Author(s)
      Arita M, Tokimatsu T
    • Journal Title

      Proceedings of the 18th International Conference on Genome Informatics (Genome Informatics Series)(Singapore) Vol.19

      Pages: 3-14

    • Peer Reviewed
  • [Journal Article] Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns2006

    • Author(s)
      Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O
    • Journal Title

      Bioinformatics 22(10)

      Pages: 1211-1216

    • Peer Reviewed
  • [Journal Article] Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes2005

    • Author(s)
      Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O
    • Journal Title

      Gene 364

      Pages: 53-62

    • Peer Reviewed
  • [Presentation] Knowledge Management using a Wiki-based System and its Application to Mass Spectra2011

    • Author(s)
      Arita M
    • Organizer
      EBI Seminar
    • Place of Presentation
      EBI, Hinxton UK
    • Year and Date
      2011-04-19
  • [Presentation] Wiki-based platform for PKS in Aspergilli2010

    • Author(s)
      Arita M
    • Organizer
      Pacifichem
    • Place of Presentation
      Honolulu (Hawaii)
    • Year and Date
      2010-12-19
  • [Presentation] Integration of Flavonoid Information through Wiki2009

    • Author(s)
      Arita M
    • Organizer
      Satellite Symposium of 4th International Conference on Polyphenols and Health (ICPH2009)
    • Place of Presentation
      Yorkshire England
    • Year and Date
      20091207-20091211
  • [Presentation] Web-based Resources for Metabolomics2009

    • Author(s)
      Arita M
    • Organizer
      Tutorial at the CBI-KSBSB joint conference (Bioinfo2009)
    • Place of Presentation
      Haeundae Busan Korea
    • Year and Date
      20091104-20091106
  • [Presentation] Data Management of Cross-disciplinary Information using Wiki2009

    • Author(s)
      Arita M
    • Organizer
      16th International Conference on Cytochrome P450
    • Place of Presentation
      Okinawa Japan
    • Year and Date
      20090621-20090625
  • [Presentation] Metabolic Pathway Analysis using Wiki2009

    • Author(s)
      Arita M
    • Organizer
      The Sixth International Aspergillus Meeting (Asperfest 6)
    • Place of Presentation
      Monterey USA
    • Year and Date
      20090315-20090317
  • [Presentation] Wiki-based Database of Secondary Metabolites2008

    • Author(s)
      Arita M
    • Organizer
      JSPS-KOSEF Joint Seminar -Pioneering researches on fungal molecular biology-
    • Place of Presentation
      Kanazawa Japan
    • Year and Date
      20081119-20081120
  • [Presentation] Computational Analysis of Metabolism2008

    • Author(s)
      Arita M
    • Organizer
      iPlant Mechanistic modeling grand challenge workshop
    • Place of Presentation
      Biosphere2 Arizona USA
    • Year and Date
      20081107-20081110
  • [Presentation] Software Tools to Study Flavonoids2007

    • Author(s)
      Arita M
    • Organizer
      Systems Biology and Bioinformatics Symposium (SBBS07)
    • Place of Presentation
      Taipei Taiwan
    • Year and Date
      20070327-20070329
  • [Presentation] Databaes for Flavonoids and Measurement in Arabidopsis2007

    • Author(s)
      Arita M
    • Organizer
      2nd International Symposium on Environmental Metabolomics
    • Place of Presentation
      University of Louisville(KY), USA
    • Year and Date
      20070324-20070325
  • [Presentation] Metabolic Pathway Chart for Flavonoid2006

    • Author(s)
      Arita M
    • Organizer
      2nd Taiwan-Japan Bilateral Symposium on Bioinformatics
    • Place of Presentation
      Tainan Taiwan
    • Year and Date
      20061107-20061109
  • [Presentation] Atomic-level analysis of metabolism and mass spectral database2006

    • Author(s)
      Arita M
    • Organizer
      Invited Lecture Course
    • Place of Presentation
      Center for Regulatory, Environmental, Analytical Metabolomics, University of Louisville(KY), USA
    • Year and Date
      20060509-20060514
  • [Presentation] Metabolomics in Japan and the Need for a Metabolic Map Editor2006

    • Author(s)
      Arita M
    • Organizer
      1st Japan-Taiwan Bilateral Symposium on Bioinformatics
    • Place of Presentation
      Tokyo Japan
    • Year and Date
      20060313-20060317
  • [Presentation] Map Editor for the Atomic Reconstruction of Metabolism2005

    • Author(s)
      Arita M
    • Organizer
      1st Louisville Symposium on Environmental Metabolomics
    • Place of Presentation
      Louisville (KY) USA
    • Year and Date
      20051105-20051106
  • [Presentation] ARM Database for Interactive Metabolic Maps2005

    • Author(s)
      Arita M
    • Organizer
      1st International BioPAX Symposium
    • Place of Presentation
      Tokyo Japan
    • Year and Date
      2005-11-18
  • [Book] 実験医学(代謝産物の検索に役立つデータベース:化合物の素性・素行を調べるウェブサイト)9月号Vol.28(14)2010

    • Author(s)
      有田正規
    • Total Pages
      2301-2303
  • [Book] Integrated omics approaches in plant systems biology(Current Opinion in Chemical Biology 13)2009

    • Author(s)
      Fukushima A, Kusano M, Redestig H, Arita M, Saito K
    • Total Pages
      532-538
  • [Book] What can metabolomics learn from genomics and proteomics?(Current Opinion in Biotechnology 20)2009

    • Author(s)
      Arita M
    • Total Pages
      610-615
  • [Book] 実験医学(植物メタボロミクス-代謝プロファイルからシステム解析へ)1月号2008

    • Author(s)
      福島敦史, 草野都, 有田正規, 斉藤和季
    • Publisher
      羊土社
  • [Book] バイオデータベースとソフトウェア最前線(「Wikiによるフラボノイドのデータベース」実験医学増刊)2008

    • Author(s)
      有田正規, 諏訪和大
    • Total Pages
      1148-1154
    • Publisher
      羊土社
  • [Book] 数理科学(生体ネットワークをどう研究するべきか)5月号(527)2007

    • Author(s)
      有田正規
    • Total Pages
      79-83
    • Publisher
      サイエンス社
  • [Book] Map Editor for the Atomic Reconstruction of Metabolism (ARM)(Eds.K Saito, RA Dixon, L Willmitzer)(Chapter II.3 In Plant Metabolomics Biotechnology in Agriculture and Forestry)Vol.572006

    • Author(s)
      Arita M, Fujiwara Y, Nakanishi Y
    • Total Pages
      129-140
    • Publisher
      Springer Verlag
  • [Book] KNApSAcK : A Comprehensive Species-Metabolite Relationship Database.(Eds.K Saito, RA Dixon, L Willmitzer)(Chapter II.6 In Plant Metabolomics Biotechnology in Agriculture and Forestry)Vol.572006

    • Author(s)
      Shinbo Y,, Arita, M., Saito, K., Ohta, D., Shibata, D., Kanaya, S.
    • Total Pages
      165-184
    • Publisher
      Springer Verlag
  • [Book] 細胞工学(代謝マップビューワで見るフラボノイド)25(12)2006

    • Author(s)
      時松敏明, 有田正規
    • Total Pages
      1388-1393
  • [Book] システム制御情報学会誌(細胞内現象のシステム的理解-今理論に何が求められているのか?」 システム/制御/情報)50(8)2006

    • Author(s)
      小林徹也, 有田正規, 森下喜弘, 合原一幸
  • [Book] ネットワーク的思考で生命現象をよみとく」(特集「意識・脳・身体の接続へ」)科学76(3)2006

    • Author(s)
      杉峰伸明, 大塚一路, 有田正規, 合原一幸
    • Publisher
      岩波書店
  • [Remarks] ソフトウェア

  • [Remarks] Flavonoid Viewer:フラボノイドの構造、分類データベース

    • URL

      http://www.metabolome.jp/software/FlavonoidViewer/

  • [Remarks] ポータル・データベース

  • [Remarks] 本研究費により作成したが、サイトをクローズする予定のポータル

    • URL

      http://metabolome.jp/

  • [Remarks] 本研究費により作成した研究成果公開用バイオポータルおよび研究室ウェブページ

    • URL

      http://metabolomics.jp/

URL: 

Published: 2012-02-13   Modified: 2016-04-21  

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