Interaction map to elucidate structural transformations in biological systems

• Project/Area Number: 17017006
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The 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
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥71,000,000 (Direct Cost: ¥71,000,000); Fiscal Year 2009: ¥15,000,000 (Direct Cost: ¥15,000,000); Fiscal Year 2008: ¥15,000,000 (Direct Cost: ¥15,000,000); Fiscal Year 2007: ¥14,800,000 (Direct Cost: ¥14,800,000); Fiscal Year 2006: ¥14,600,000 (Direct Cost: ¥14,600,000); Fiscal Year 2005: ¥11,600,000 (Direct Cost: ¥11,600,000)
• Keywords: 代謝 / データベース / フラボノイド / バイオポータル / 進化モデル / ノイズ / 分子構造 / 脂質 / 質量分析 / 化合物データベース

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

• [Journal Article] Reconstructing phylogeny from metabolic substrate-product relationships (2011)
  • Author(s): Chang CW, Lyu PC, Arita M
  • Journal Title: BMC Bioinformatics (Proceedings 9th APBC in Korea) 12(Suppl 1)
  • Peer Reviewed
• [Journal Article] Multi-stage mass spectrometric analysis of saponins in glycyrrhiza radix (2011)
  • Author(s): Tanaka K, Hayashi K, Fahad A, Arita M
  • Journal Title: Natural Product Communications Volume: 6:1 Pages: 7-10
  • Peer Reviewed
• [Journal Article] Reconstructing phylogeny from metabolic substrate-product relationships (2011)
  • Author(s): Chang CW, Lyu PC, Arita M
  • Journal Title: BMC Bioinformatics Volume: 12(Suppl 1)
  • Peer Reviewed
• [Journal Article] Noise-intensity fluctuation in Langevin model and its higher-order Fokker-Planck equation (2011)
  • Author(s): Hasegawa Y, Arita M
  • Journal Title: Physica A Volume: 390(6) Pages: 1051-1063
  • Peer Reviewed
• [Journal Article] Nested structure acquired through simple evolutionary process (2010)
  • 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 family (2010)
  • Author(s): Hasegawa Y, Arita M
  • Journal Title: Physica A 389(21) Pages: 4450-4461
  • Peer Reviewed
• [Journal Article] Nested structure acquired through simple evolutionary process (2010)
  • Author(s): Takemoto K, Arita M
  • Journal Title: Journal of Theoretical Biology Volume: 264 Pages: 782-786
  • Peer Reviewed
• [Journal Article] Bistable stochastic processes in the q-exponential family (2010)
  • Author(s): Hasegawa Y, Arita M
  • Journal Title: Physica A Volume: 389(21) Pages: 4450-4461
  • Peer Reviewed
• [Journal Article] A pitfall of wiki solution for biological databases (2009)
  • Author(s): Arita M
  • Journal Title: Briefings Bioinformatics 10(3) Pages: 295-296
  • Peer Reviewed
• [Journal Article] Heterogeneous distribution of metabolites across plant species (2009)
  • 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 annotations (2009)
  • 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 information (2009)
  • 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 variables (2009)
  • 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 approach (2009)
  • Author(s): Fukushima A, Kanaya S, Arita M
  • Journal Title: Plant Biotechnology 26 Pages: 485-493
  • NAID: 10026136448
  • Peer Reviewed
• [Journal Article] Period-phase map : two-dimensional selection of circadian rhythm-related genes (2009)
  • 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 foliage (2008)
  • Author(s): Sato S, Arita M M, Soga T, Nishioka T, Tomita M
  • Journal Title: BMC Systems Biology 2 Pages: 51-51
  • Peer Reviewed
• [Journal Article] Search extension transforms Wiki into a relational system : a case for flavonoid metabolite database (2008)
  • Author(s): Arita M, Suwa K
  • Journal Title: BMC BioData Mining 1 Pages: 7-7
  • Peer Reviewed
• [Journal Article] SVD-based anatomy of gene-expression for correlation analysis in Arabidopsis thaliana (2008)
  • Author(s): Fukushima A, Wada M, Kanaya S, Arita M
  • Journal Title: DNA research 15(6) Pages: 367-374
  • Peer Reviewed
• [Journal Article] Time-resolved metabolomics reveals metabolic modulation in rice foliage (2008)
  • Author(s): Shigeru Sato
  • Journal Title: BMC Systems Biology 2 Pages: 51-51
  • Peer Reviewed
• [Journal Article] 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 (2008)
  • Author(s): 福島敦史
  • Journal Title: 実験医学, 1月号 1
• [Journal Article] Wikiによるフラボノイドのデータベース (2008)
  • Author(s): 有田正規
  • Journal Title: 実験医学増刊,「バイオデータベースとソフトウェア最前線」,4月 n/a Pages: 1148-1154
• [Journal Article] Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions (2007)
  • 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 coordinates (2007)
  • 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
  • NAID: 130003812171
  • Peer Reviewed
• [Journal Article] Detection of monosaccharide types from coordinates (2007)
  • Author(s): Masanori Arita
  • Journal Title: Proceedings of the 18th International Conference on Genome In formatics (Genome Informatics Series 19) 19 Pages: 3-14
  • NAID: 130003812171
  • Peer Reviewed
• [Journal Article] Unbiased characterization of genotype-dependent metabolic regulations by metabolo mic approach in Arabidopsis thaliana (2007)
  • Author(s): Miyako Kusano
  • Journal Title: BMC Systems Biology 1 Pages: 53-53
  • Peer Reviewed
• [Journal Article] 生体ネットワークをどう研究するべきか (2007)
  • Author(s): 有田正規
  • Journal Title: 数理科学5月号 527 Pages: 79-83
• [Journal Article] Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions (2007)
  • Author(s): Kinya Okada
  • Journal Title: Proceedings of 5th Asia Pacific Bioinformatics Conference(APBC2007) 6
• [Journal Article] Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns (2006)
  • Author(s): Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O
  • Journal Title: Bioinformatics 22(10) Pages: 1211-1216
  • Peer Reviewed
• [Journal Article] Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns (2006)
  • Author(s): Hideki Nagasaki
  • Journal Title: Bioinformatics 22(10) Pages: 1211-1211
• [Journal Article] Comparison of Protein Complexes Predicted from PPI Networks by DPClus and Newman Clustering Algorithms (2006)
  • Author(s): Hiroshi Tsuji
  • Journal Title: IPSJ Transactions on Bioinformatics 47 Pages: 31-31
• [Journal Article] Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes (2005)
  • Author(s): Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O
  • Journal Title: Gene 364 Pages: 53-62
  • Peer Reviewed
• [Journal Article] Scale-freeness and biological networks (2005)
  • Author(s): Arita, M
  • Journal Title: Journal of Biochemistry 138 Pages: 1-4
  • NAID: 10017345784
• [Journal Article] All systems go : launching cell simulation fueled by integrated experimental biology data (2005)
  • Author(s): Arita, M., Robert, M., Tomita, M.
  • Journal Title: Current Opinion in Biotechnology 16(3) Pages: 344-349
• [Journal Article] メタボロームによる脂質代謝パスウェイ解析 (2005)
  • Author(s): 有田 正規, 田口 良
  • Journal Title: 実験医学増刊号「ダイナミックに新展開する脂質研究」 23(6) Pages: 151-157
• [Presentation] Knowledge Management using a Wiki-based System and its Application to Mass Spectra (2011)
  • 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 Aspergilli (2010)
  • Author(s): Arita M
  • Organizer: Pacifichem 2010
  • Place of Presentation: ハワイ、ホノルル USA
  • Year and Date: 2010-12-20
• [Presentation] Wiki-based platform for PKS in Aspergilli (2010)
  • Author(s): Arita M
  • Organizer: Pacifichem
  • Place of Presentation: Honolulu (Hawaii)
  • Year and Date: 2010-12-19
• [Presentation] Database for crude drugs and Kampo medicine (2010)
  • Author(s): Arita M
  • Organizer: 日本バイオインフォマティクス学会年会
  • Place of Presentation: 福岡 九州大学
  • Year and Date: 2010-12-13
• [Presentation] ウェブを通じた生薬知識のアウトリーチ (2010)
  • Author(s): 有田正規
  • Organizer: 南方資源研究会
  • Place of Presentation: 沖縄、那覇
  • Year and Date: 2010-11-26
• [Presentation] 細胞内のノイズと遺伝子スイッチ (2010)
  • Author(s): 長谷川禎彦、有田正規
  • Organizer: 細胞を創る研究会
  • Place of Presentation: 東京、東大駒場
  • Year and Date: 2010-11-12
• [Presentation] Metabolic Pathway Analysis using Wiki (2009)
  • Author(s): Arita M
  • Organizer: The Sixth International Aspergillus Meeting (Asperfest 6)
  • Place of Presentation: Monterey USA
• [Presentation] Data Management of Cross-disciplinary Information using Wiki (2009)
  • Author(s): Arita M
  • Organizer: 16th International Conference on Cytochrome P450
  • Place of Presentation: Okinawa Japan
• [Presentation] Web-based Resources for Metabolomics (2009)
  • Author(s): Arita M
  • Organizer: Tutorial at the CBI-KSBSB joint conference (Bioinfo2009)
  • Place of Presentation: Haeundae Busan Korea
• [Presentation] Integration of Flavonoid Information through Wiki (2009)
  • Author(s): Arita M
  • Organizer: Satellite Symposium of 4th International Conference on Polyphenols and Health (ICPH2009)
  • Place of Presentation: Yorkshire England
• [Presentation] Computational Analysis of Metabolism (2008)
  • Author(s): Arita M
  • Organizer: iPlant Mechanistic modeling grand challenge workshop
  • Place of Presentation: Biosphere2 Arizona USA
• [Presentation] Wiki-based Database of Secondary Metabolites (2008)
  • Author(s): Arita M
  • Organizer: JSPS-KOSEF Joint Seminar -Pioneering researches on fungal molecular biology-
  • Place of Presentation: Kanazawa Japan
• [Presentation] Databaes for Flavonoids and Measurement in Arabidopsis (2007)
  • Author(s): Arita M
  • Organizer: 2nd International Symposium on Environmental Metabolomics
  • Place of Presentation: University of Louisville(KY), USA
• [Presentation] Software Tools to Study Flavonoids (2007)
  • Author(s): Arita M
  • Organizer: Systems Biology and Bioinformatics Symposium (SBBS07)
  • Place of Presentation: Taipei Taiwan
• [Presentation] Metabolomics in Japan and the Need for a Metabolic Map Editor (2006)
  • Author(s): Arita M
  • Organizer: 1st Japan-Taiwan Bilateral Symposium on Bioinformatics
  • Place of Presentation: Tokyo Japan
• [Presentation] Atomic-level analysis of metabolism and mass spectral database (2006)
  • Author(s): Arita M
  • Organizer: Invited Lecture Course
  • Place of Presentation: Center for Regulatory, Environmental, Analytical Metabolomics, University of Louisville(KY), USA
• [Presentation] Metabolic Pathway Chart for Flavonoid (2006)
  • Author(s): Arita M
  • Organizer: 2nd Taiwan-Japan Bilateral Symposium on Bioinformatics
  • Place of Presentation: Tainan Taiwan
• [Presentation] ARM Database for Interactive Metabolic Maps (2005)
  • Author(s): Arita M
  • Organizer: 1st International BioPAX Symposium
  • Place of Presentation: Tokyo Japan
  • Year and Date: 2005-11-18
• [Presentation] Map Editor for the Atomic Reconstruction of Metabolism (2005)
  • Author(s): Arita M
  • Organizer: 1st Louisville Symposium on Environmental Metabolomics
  • Place of Presentation: Louisville (KY) USA
• [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
• [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
• [Book] What can metabolomics learn from genomics and proteomics?(Current Opinion in Biotechnology 20) (2009)
  • Author(s): Arita M
• [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
  • 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
  • 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.57 (2006)
  • Author(s): Arita M, Fujiwara Y, Nakanishi Y
  • 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.57 (2006)
  • Author(s): Shinbo Y,, Arita, M., Saito, K., Ohta, D., Shibata, D., Kanaya, S.
  • 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
• [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
• [Book] Introduction to the ARM Database : Database on Chemical Transformations in Metabolism for Tracing Pathways (Chapter 13 in "Metabolomics : The Frontier of Systems Biology") (2005)
  • Author(s): Arita, M
  • Total Pages: 19
  • Publisher: Springer verlag
• [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/
• [Remarks]
  • URL: http://metabolomics.jp/
• [Remarks]
  • URL: http://lipidbank.jp/
• [Remarks]
  • URL: http://metabolome.jp/
• [Remarks]
  • URL: http://metabolomics.jp/