KEGG Database
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database resource that integrates genomic, chemical and systemic functional information. In particular, gene catalogs from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism and the ecosystem.
Major efforts have been undertaken to manually create a knowledge base for such systemic functions by capturing and organizing experimental knowledge in computable forms; namely, in the forms of molecular networks called KEGG pathway maps, BRITE functional hierarchies and KEGG modules. Continuous efforts have also been made to develop and improve the cross-species annotation procedure for linking genomes to the molecular networks through the KEGG Orthology (KO) system.
As the result, KEGG is widely used as a reference knowledge base for integration and interpretation of large-scale datasets generated by genome sequencing and other high-throughput experimental technologies. In addition to maintaining the aspects to support basic research, KEGG is being expanded towards more practical applications integrating human diseases, drugs and other health-related substances as perturbations of the KEGG molecular networks.
KEGG is developed by Kanehisa Laboratories.
Please cite the following article(s) when using KEGG.
Major efforts have been undertaken to manually create a knowledge base for such systemic functions by capturing and organizing experimental knowledge in computable forms; namely, in the forms of molecular networks called KEGG pathway maps, BRITE functional hierarchies and KEGG modules. Continuous efforts have also been made to develop and improve the cross-species annotation procedure for linking genomes to the molecular networks through the KEGG Orthology (KO) system.
As the result, KEGG is widely used as a reference knowledge base for integration and interpretation of large-scale datasets generated by genome sequencing and other high-throughput experimental technologies. In addition to maintaining the aspects to support basic research, KEGG is being expanded towards more practical applications integrating human diseases, drugs and other health-related substances as perturbations of the KEGG molecular networks.
KEGG is developed by Kanehisa Laboratories.
Please cite the following article(s) when using KEGG.
- Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., and Tanabe, M.; KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res. 40, D109-D114 (2012). [pubmed] [pdf]
- Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [pubmed] [pdf]
Please see the following for background and basic concepts of KEGG.
- Kanehisa, M.; "Post-genome Informatics", Oxford University Press (2000). [Preface] [Table of Contents]
References on KEGG
- Kanehisa, M.; Toward pathway engineering: a new database of genetic and molecular pathways. Science & Technology Japan, No. 59, pp. 34-38 (1996). [pdf]
- 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]
- Kanehisa, M.; A database for post-genome analysis. Trends Genet. 13, 375-376 (1997). [pubmed]
- 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]
- Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [pubmed] [pdf]
- Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A.; The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002). [pubmed] [pdf]
- Kanehisa, M.; The KEGG database. Novartis Found. Symp. 247, 91-101 (2002). [pubmed]
- 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]
- 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., 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]
- 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., Sato, Y., Furumichi, M., and Tanabe, M.; KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res. 40, D109-D114 (2012). [pubmed] [pdf]
References on Analyses and Algorithms
See the publication list of Minoru Kanehisa.
References on DBGET/LinkDB
- 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]
- 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]
- Kanehisa, M.; Linking databases and organisms: GenomeNet resources in Japan. Trends Biochem Sci. 22, 442-444 (1997). [pubmed]
- 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]
References on LIGAND
- Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: chemical database for enzyme reactions. Bioinformatics 14, 591-599 (1998). [pubmed]
- Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND database for enzymes, compounds, and reactions. Nucleic Acids Res. 27, 377-379 (1999). [pubmed]
- Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: chemical database of enzyme reactions. Nucleic Acids Res. 28, 380-382 (2000). [pubmed]
- 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
- 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]
Acknowledgments
| The KEGG project is partially supported by: |
- Life Science Database Integration Project (2011-2013) of the National Bioscience Database Center, Japan Science and Technology Agency
| The computational resources are provided by: |
- Bioinformatics Center, the Institute for Chemical Research, Kyoto University
| Past supports include: |
- Grand-in-aid for scientific research on the priority area "Genome Informatics" (1995) from the Ministry of Education
- Grand-in-aid for scientific research on the priority area "Genome Science" (1996-2000) from the Ministry of Education
- Research for the Future Program (2000-2004) from the Japan Society for the Promotion of Science
- Bioinformatics Research and Development (2001-2005) of the Japan Science and Technology Agency
- 21st Century COE Program "Genome Science" (2003-2007) from the Ministry of Education
- Grant-in-aid for scientific research on the priority area "Comprehensive Genomics" (2005-2009) from the Ministry of Education
- Bioinformatics Research and Development (2006-2010) of the Japan Science and Technology Agency
| More details of each project can be found in the Kanehisa Laboratories Archive. |
Last updated: October 1, 2012