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Biological Knowledge Based on Genome Information

Research Project

Project/Area Number 08283103
Research Category

Grant-in-Aid for Scientific Research on Priority Areas (A)

Allocation TypeSingle-year Grants
Research InstitutionKYOTO UNIVERSITY

Principal Investigator

KANEHISA Minoru  Institute for Chemical Research, Professor, 化学研究所, 教授 (70183275)

Co-Investigator(Kenkyū-buntansha) KUHARA Satoru  Kyushu University, Graduate School of Genetic Resources Technology, Professor, 大学院・農学研究院, 教授 (00153320)
MIYANO Satoru  University of Tokyo. Institute of Medical Science, Professor, 医科学研究所, 教授 (50128104)
TAKAGI Toshihisa  University of Tokyo, Institute of Medical Seience, Professor, 医科学研究所, 教授 (30110836)
AKUTSU Tatsuya  University of Tokyo, Institute of Medical Science, Associate Professor, 医科学研究所, 助教授 (90261859)
MATSUDA Hideo  Osaka University, Graduate School of Engineering Science, Associate Professor, 大学院・基礎工学研究科, 助教授 (50183950)
浅井 潔  電子技術総合研究所, 知能情報部, 主任研究官
中井 謙太  大阪大学, 細胞生体工学センター, 助教授 (60217643)
森 浩禎  奈良先端科学技術大学院大学, 遺伝子教育研究センター, 教授 (90182203)
蓑島 伸生  慶應義塾大学, 医学部, 講師 (90181966)
Project Period (FY) 1996 – 2000
Project Status Completed (Fiscal Year 2000)
Budget Amount *help
¥867,600,000 (Direct Cost: ¥867,600,000)
Fiscal Year 2000: ¥167,000,000 (Direct Cost: ¥167,000,000)
Fiscal Year 1999: ¥177,000,000 (Direct Cost: ¥177,000,000)
Fiscal Year 1998: ¥176,000,000 (Direct Cost: ¥176,000,000)
Fiscal Year 1997: ¥173,600,000 (Direct Cost: ¥173,600,000)
Fiscal Year 1996: ¥174,000,000 (Direct Cost: ¥174,000,000)
KeywordsGenome analysis / Gene function prediction / Protein structure prediction / Database / Network / Molecular interactions / Pathway / Genetic diseases / 配列解析
Research Abstract

While the complete genome sequences of a number of organisms, as well as the raft sequences of the human genome, have already been determined, functional properties are not well characterized for roughly a half of the genes in each genome. This project aimed at developing bioinformatics technologies for understanding hihgher order functional meanings and utilities of the cell or the organism from its genome information. Specifically, (1) we developed a reference database named KEGG, which contains current knowledge on protein interaction networks such as metabolic pathways, various regulatory pathways, and molecular complexes. We performed prediction of protein networks and associated cellular functions for the genomes of over 50 species. (2) We developed information technology to extract knowledge on protein names and protein-protein interactions from the text in scientific literature. (3) We developed information technology to analyze gene expression profile data, such as for detecting coexpression clusters and for predicting gene regulatory networks. (4) We continued to develop mutation database for disease related genes. The project has been instrumental in further developing the GenomeNet database service as the informatics infrastructure for biomedical research in Japan and in nurturing the bioinformatics research community by regularly organizing workshops and tutorials. The basic research results, as well as the practical database products such as KEGG, are freely made available at the GenomeNet (http://www.genome.ad.jp).

Report

(6 results)
  • 2000 Annual Research Report   Final Research Report Summary
  • 1999 Annual Research Report
  • 1998 Annual Research Report
  • 1997 Annual Research Report
  • 1996 Annual Research Report
  • Research Products

    (52 results)

All Other

All Publications (52 results)

  • [Publications] Ogata, H., Fujibuchi, W., Goto, S., Kanehisa, M.: "A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters"Nucleic Acids Research. 28. 4021-4028 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Fujibuchi, W., Ogata, H., Matsuda, H., Kanehisa, M.: "Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping"Nucleic Acids Research. 28. 4029-4036 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Yoshida, M., Fukuda, K., Takagi, T.: "PNAD-CSS : a workbench for constructing a protein name abbreviation dictionary"Bioinformatics. 16. 169-175 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Ono, T., Hishigaki, H., Tanigami, A., Takagi, T.: "Automated extraction of information on protein-protein interactions from biological literature"Bioinformatics. 17. 155-161 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Akutsu, T., Miyano, S., Kuhara, S.: "Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function"Journal of Computational Biology. 7. 331-343 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Akutsu, T.Miyano, S., Kuhara, S.: "Inferring qualitative relations in genetic networks"Bioinformatics. 16. 727-734 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Kanehisa, M.: "Post-genome Informtics"Oxford University Press. 148 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Ogata, H., Fujibuchi, W., Goto, S., Kanehisa, M: "A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters"Nucleic Acids Research. 28. 4021-4028 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Fujibuchi, W., Ogata, H., Matsuda, H., Kanehisa, M.: "Automatic detection of conserved gene clusters in multiple genomes by graph comparison amd P-quasi grouping"Nucleic Acids Research. 28. 4029-4036 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Yoshida, M., Fukuda, K., and Takagi, T.: "PNAD-CSS : a workbench for constructing a protein name abbreviation dictionary"Bioinfomatics. 16. 169-175 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Ono, T., Hishigaki, H., Tanigami, and A., Takagi, T.: "Automated extraction of information on protein-protein interactions from biological litetature"Bioinformatics. 17. 155-161 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Akutsu, T., Miyano, S., and Kuhara, S.: "Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function"Journal of Computational Biology. 7. 331-343 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Akutsu, T., Miyano, S., and Kuhara, S.: "Inferring qualitative relations in genetic networks"Bioinformatics. 16. 727-734 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Kanehisa, M.: "Oxford University Press."Post-genome Informtics. 148 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] Ogata,H.,Fujibuchi,W.,Goto,S.,Kanehisa,M.: "A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters"Nucleic Acids Research. 28. 4021-4028 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Fujibuchi,W.,Ogata,H.,Matsuda,H.,Kanehisa,M.: "Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping"Nucleic Acids Research. 28. 4029-4036 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Yoshida,M.,Fukuda,K.and Takagi,T.: "PNAD-CSS : a workbench for constructing a protein name abbreviation dictionary"Bioinformatics. 16. 169-175 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Ono,T.,Hishigaki,H.,Tanigami,A.and Takagi,T.: "Automated extraction of information on protein-protein interactions from biological literature"Bioinformatics. 17. 155-161 (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Akutsu,T.,Miyano,S.and Kuhara,S.: "Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function"Journal of Computational Biology. 7. 331-343 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Akutsu,T.,Miyano,S.and Kuhara,S.: "Inferring qualitative relations in genetic networks"Bioinformatics. 16. 727-734 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Kanehisa,M.: "Post-genome Informtics"Oxford University Press. 148 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Dunker,A.K.,Konagaya,A.,Miyano,S.,Takagi,T.: "Genome Informatics 2000"Universal Academy Press,Inc.. 472 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Kanehisa, M. and Goto, S.: "KEGG : Kyoto Encyclopedia of Genes and Genomes"Nucleic Acids Research. 28. 27-30 (2000)

    • Related Report
      1999 Annual Research Report
  • [Publications] Goto, S., Nishioka, T. and Kanehisa, M.: "LIGAND : chemical database for enzyme reactions"Nucleic Acids Research. 28. 380-382 (2000)

    • Related Report
      1999 Annual Research Report
  • [Publications] Tsunoda, T. and Takagi, T.: "Estimating transcription factor bindability on DNA"Bioinformatics. 15. 622-630 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Matsuno, H., Doi, A., Nagasaki, M., and Miyano, S.: "Hybrid Petri net representation of gene regulatory network"Pacific. Symp. Biocomput.. 5. 341-352 (2000)

    • Related Report
      1999 Annual Research Report
  • [Publications] matsuda, H., Ishihara, T., Hashimoto, A.: "Classifying molecular sequences using a linkage graph with their pairwise similarities"Theoret. Comput. Sci.. 210. 305-325 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Akutsu, T. and Miyano, S.: "On the approximation of protein threading"Theoret. Comput. Sci.. 210. 261-275 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Kanehisa, M.: "Post-genome Informatics"Oxford University Press. 148 (2000)

    • Related Report
      1999 Annual Research Report
  • [Publications] Asai, K., Miyano, S. and Takagi, T.: "Genome Informatics Workshop 1999"Universal Academy Press, Inc.. 373 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Bono,H., Ogata,H., Kanehisa,M.他: "Reconstruction of amino acid biosynthesis pathways from the complete genome sequence." Genome Research. 8. 203-210 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Tomii,K.and Kanehisa,M.Kanehisa,M.他: "A comparative analysis of ABC transporters in the complete microbial genomes" Genome Research. 8. 1048-1059 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Kihara,D., Shimizu,T., and Kanehisa,M.: "Prediction of membrane proteins based on classification of transmembrane segments." Protein Engineering. 11. 961-970 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Murakami,K.and Takagi,T.: "Gene recognition by combination of several gene-finding programs" Bioinformatics. 14. 665-675 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Yada,T., Asai,K., Naki,K.他: "Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences" Bioinformatics. 14. 317-325 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Akutsu,T.and Tashimo,H.: "Linear programming based approach to the derivation of a contact potential for protein threading" Pacific.Symp.Biocomput.3. 413-424 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Miyano,S.and Takagi,T.: "Genome Informatics Workshop 1998" Universal Academy Press,Inc., 400 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] 高木利久、金久 實: "ゲノムネットのデータベース利用法[第2版]" 共立出版, 206 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Kanehisa, M.: "Linking databases and organisms : GenomeNet resources in Japan." Trende Biochem Sci.22. 442-444 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Fujibuchi,W., Goto,S., Kanehisa,M.他: "DBGET/LinkDB : an integrated database retrieval system." Proc.Pacific Symposium on Biocomputing'98. 683-694 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Ohta,Y., Yamamoto,Y., Takagi,T.他: "Automatic construction of knowledge base from biological papers." ISMB. 5. 218-225 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Miyano,S.: "Genome Informatics : new frontiers of computer science and biosciences." Cooperative Databases and Applications. 12-21 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Tsukamoto,Y., Takagi,T., Kuhara,S.他.: "Application of a deductive database system for topological and similar three dimensional structures in protein" CABIOS. 13. 183-190 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Akutsu,T., Onizuka,K., Ishikawa,M.: "Rapid protein fragment search using hash functions based on the fourier transform." CABIOS. 13. 357-364 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Miyano,S. and Takagi,T.: "Genome Informatics Workshop 1997" Universal Academy Press,Inc., 365 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Kanehisa,M.: "Toward pathway engineering : a new database of genetic and molecular pathways." Science & Technology Japan. 59. 34-38 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Gotoh,S.,Kanehisa,M.他: "Organizing and computing metabolic pathway data in terms of binary relations." Proc.Pacific Symposium on Biocomputing'97. 175-186 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Satou,K.,Takagi,T.他: "Finding association rules on heterogeneous genome data." Proc.Pacific Symposium on Biocomputing'97. 397-408 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Tateishi,E.,Maruyama,O.,Miyano,S.: "Extracting best consensus motifs from positive and negative examples." Lecture Notes in Computer Science. 1046. 219-230 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Akutsu,T.: "Protein structure alignment using dynamic programming and iterarive improvement." IEICE Trans.Information and Systems. E79-D. 1629-1636 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Matsuda,H.,Taniguchi,F.,Hashimoto,A.: "An approach to detection of protein structural motifs using an encoding scheme of backbone conformations." Proc.Pacific Symposium on Biocomputing'97. 280-291 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Akutsu,T.,Asai,K.,Hagiya,M.,Kuhara,S.,Miyano,S.,Nakai,N.: "Proceedings of Genome Informatics Workshop 1996" Universal Academy Press,Inc., 284 (1996)

    • Related Report
      1996 Annual Research Report

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Published: 1996-04-01   Modified: 2016-04-21  

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