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Introduction to KEGG

The increasing amount of genome sequence data is the basis for understanding life as a molecular system and for developing medical, pharmaceutical, and other practical applications. Since 1995 we have been developing knowledge-based methods for uncovering higher-order systemic behaviors of the cell and the organism from genomic and molecular information. The reference knowledge is stored in KEGG, Kyoto Encyclopedia of Genes and Genomes, and associated bioinformatics technologies are being developed both for basic research and practical applications.

See Overview for more details.
See Kanehisa Laboratory for the people involved.

Please cite the following article(s) when using KEGG.
  • Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010). [pubmed] [pdf]
  • Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006). [pubmed] [pdf] [Thomson]
  • Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [pubmed] [pdf]

Documents

References on KEGG

  1. Kanehisa, M.; Toward pathway engineering: a new database of genetic and molecular pathways. Science & Technology Japan, No. 59, pp. 34-38 (1996). [pdf]
  2. Kanehisa, M. and Goto, S.; A systematic analysis of gene functions by the metabolic pathway database. In "Theoretical and Computational Methods in Genome Research" (Suhai, S., ed.), pp. 41-55, Plenum Press (1997). [ISBN:0-306-45503-X]
  3. Goto, S., Bono, H., Ogata, H., Fujibuchi, W., Nishioka, T., Sato, K., and Kanehisa, M.; Organizing and computing metabolic pathway data in terms of binary relations. Pacific Symp. Biocomputing 1997, 175-186 (1996). [pubmed] [pdf]
  4. Kanehisa, M.; A database for post-genome analysis. Trends Genet. 13, 375-376 (1997). [pubmed]
  5. Kanehisa, M.; Databases of biological information. In "Trends Guide to Bioinformatics" (Brenner, S. and Lewitter, F., eds.), pp. 24-26, Elsevier Science (1998).
  6. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29-34 (1999). [pubmed] [pdf]
  7. Kanehisa, M.; KEGG: From genes to biochemical pathways. In "Bioinfomatics: Databases and Systems" (Letovsky, S., ed.), pp. 63-76, Kluwer Academic Publishers (1999). [ISBN:0-7923-8573-X]
  8. Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [pubmed] [pdf]
  9. Kanehisa, M.; "Post-genome Informatics", Oxford University Press (2000). [ISBN:0-19-850327-X] [Preface] [Contents]
  10. Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A.; The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002). [pubmed] [pdf]
  11. Kanehisa, M. and Goto, S.; KEGG for computational genomics. In "Current Topics in Computational Molecular Biology" (Jiang, T., Xu, Y., and Zhang, M.Q., eds.), pp. 301-315, MIT-Press, Cambridge, MA (2002). [ISBN:0-262-10092-4]
  12. Kanehisa, M.; The KEGG database. Novartis Found. Symp. 247, 91-101 (2002). [pubmed]
  13. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M.; The KEGG resources for deciphering the genome. Nucleic Acids Res. 32, D277-D280 (2004). [pubmed] [pdf]
  14. Aoki, K.F. and Kanehisa, M.; Using the KEGG Database Resource. In "Current Protocols in Bioinformatics", Unit 1.12, Wiley (2005).
  15. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006). [pubmed] [pdf] [Thomson]
  16. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., and Yamanishi, Y.; KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-D484 (2008). [pubmed] [pdf]
  17. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010). [pubmed] [pdf]

References on Analyses and Algorithms

See the publication list of the Kanehisa Laboratory.

References on DBGET/LinkDB

  1. Akiyama, Y., Goto, S., Uchiyama, I., and Kanehisa, M.; WebDBGET: an integrated database retrieval system which provides hyper-links among related entries. MIMBD'95: Second Meeting on the Interconnection of Molecular Biology Databases (1995). [pdf]
  2. Goto, S., Akiyama, Y., and Kanehisa, M.; LinkDB: a database of cross links between molecular biology databases. MIMBD'95: Second Meeting on the Interconnection of Molecular Biology Databases (1995). [pdf]
  3. Kanehisa, M.; Linking databases and organisms: GenomeNet resources in Japan. Trends Biochem Sci. 22, 442-444 (1997). [pubmed]
  4. Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.; DBGET/LinkDB: an integrated database retrieval system. Pacific Symp. Biocomputing 1998, 683-694 (1997). [pubmed] [pdf]
  5. Fujibuchi, W., Sato, K., Ogata, H., Goto, S., and Kanehisa, M.; KEGG and DBGET/LinkDB: Integration of biological relationships in divergenet molecular biology data. In "Knowledge Sharing Across Biological and Medical Knowledge Based Systems", Technical Report WS-98-04, pp. 35-40, AAAI Press (1998).

References on LIGAND

  1. Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: chemical database for enzyme reactions. Bioinformatics 14, 591-599 (1998). [pubmed]
  2. Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND database for enzymes, compounds, and reactions. Nucleic Acids Res. 27, 377-379 (1999). [pubmed]
  3. Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: chemical database of enzyme reactions. Nucleic Acids Res. 28, 380-382 (2000). [pubmed]
  4. Goto, S., Okuno, Y., Hattori, M., Nishioka, T. and Kanehisa, M.; LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30, 402-404 (2002). [pubmed]

Reference on GLYCAN

  1. Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., Kawasaki, T., and Kanehisa, M.; KEGG as a glycome informatics resource. Glycobiology 16, 63R-70R (2006). [pubmed]

Project Team

  • Project Leader: Minoru Kanehisa
  • Small molecule metabolism: Tomoko Komeno, Rumiko Yamamoto, Yuriko Matsuura, Atsuko Yoda, Waka Masuyama, Masahiro Hattori, Masaaki Kotera
  • Glycan/lipid metabolism: Masami Hamajima
  • Plant metabolism: Etsuko Terajima, Hiromi Kinoshita, Toshiaki Tokimatsu
  • Biological processes and diseases: Atsuko Yano, Mao Tanabe, Aya Ito, Akiko Hashiguchi, Mika Hirakawa
  • Drug information: Mari Watanabe, Makiko Ogata, Fumi Kiuchi
  • KO grouping: Miho Furumichi
  • Genome/pathway annotation: Tomomi Kamiya, Mayo Ishii, Shiho Ikeuchi, Kanae Morishima, Etsuko Sano
  • System Development: Susumu Goto, Yoko Sato (FJQS), Masayuki Kawasima (FJQS), Junya Ohori (FJQS), Satoshi Miyazaki (FNS), Koichi Ohkubo (SGI), Hideya Uehara (SGI), Kentaro Ozawa (SGI), Toshiaki Katayama, Shuichi Kawashima
  • Public relations: Miwako Karikomi, Yuko Kato
  • Administrative assistants: Kaede Yukawa, Junko Nishida

Acknowledgments

The KEGG project is currently supported by:
  • Bioinformatics Research and Development (2006-2010) of the Japan Science and Technology Agency
  • Grant-in-aid for scientific research on the priority area "Comprehensive Genomics" (2005-2009) from the Ministry of Education
The computational resources are provided by:
Past supports include:
More details of each project can be found in the Kanehisa Laboratory Archive.

Last updated: January 1, 2010
Copyright 1995-2010 Kanehisa Laboratories