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Nucleic Acids Research Advance Access published online on December 12, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm882
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

KEGG for linking genomes to life and the environment

Minoru Kanehisa1,2,*, Michihiro Araki2, Susumu Goto1, Masahiro Hattori1, Mika Hirakawa1,3, Masumi Itoh1, Toshiaki Katayama2, Shuichi Kawashima2, Shujiro Okuda1, Toshiaki Tokimatsu1 and Yoshihiro Yamanishi1

1Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, 2Human Genome Center, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639 and 3Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-8666, Japan

*To whom correspondence should be addressed: Tel: +81 774 38 3270; Fax: +81 774 38 3269; Email: kanehisa{at}kuicr.kyoto-u.ac.jp

Received September 13, 2007. Revised September 30, 2007. Accepted October 1, 2007.

KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. In addition, smaller pathway modules are defined and stored in KEGG MODULE that also contains other functional units and complexes. The KEGG resource is being expanded to suit the needs for practical applications. KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.


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J. Yu and R. L. Finley Jr
Combining multiple positive training sets to generate confidence scores for protein-protein interactions
Bioinformatics, January 1, 2009; 25(1): 105 - 111.
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 Plant Cell PhysiolHome page
Y. Ogata, N. Sakurai, K. Aoki, H. Suzuki, K. Okazaki, K. Saito, and D. Shibata
KAGIANA: An Excel-Based Tool for Retrieving Summary Information on Arabidopsis Genes
Plant Cell Physiol., January 1, 2009; 50(1): 173 - 177.
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 Nucleic Acids ResHome page
A. P. Davis, C. G. Murphy, C. A. Saraceni-Richards, M. C. Rosenstein, T. C. Wiegers, and C. J. Mattingly
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D786 - D792.
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C.-Y. Li, Q.-R. Liu, P.-W. Zhang, X.-M. Li, L. Wei, and G. R. Uhl
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D251 - D260.
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 Nucleic Acids ResHome page
C. F. Schaefer, K. Anthony, S. Krupa, J. Buchoff, M. Day, T. Hannay, and K. H. Buetow
PID: the Pathway Interaction Database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D674 - D679.
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 Nucleic Acids ResHome page
B. Liu and M. Pop
ARDB--Antibiotic Resistance Genes Database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D443 - D447.
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A. Zerlotini, M. Heiges, H. Wang, R. L. V. Moraes, A. J. Dominitini, J. C. Ruiz, J. C. Kissinger, and G. Oliveira
SchistoDB: a Schistosoma mansoni genome resource
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D579 - D582.
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 Nucleic Acids ResHome page
J. Klein, R. Munch, I. Biegler, I. Haddad, I. Retter, and D. Jahn
Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform 'Open Genome Resource' (OGeR)
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D494 - D498.
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W. Klimke, R. Agarwala, A. Badretdin, S. Chetvernin, S. Ciufo, B. Fedorov, B. Kiryutin, K. O'Neill, W. Resch, S. Resenchuk, et al.
The National Center for Biotechnology Information's Protein Clusters Database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D216 - D223.
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L. J. Jensen, M. Kuhn, M. Stark, S. Chaffron, C. Creevey, J. Muller, T. Doerks, P. Julien, A. Roth, M. Simonovic, et al.
STRING 8--a global view on proteins and their functional interactions in 630 organisms
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D412 - D416.
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T. Obayashi, S. Hayashi, M. Saeki, H. Ohta, and K. Kinoshita
ATTED-II provides coexpressed gene networks for Arabidopsis
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D987 - D991.
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S.-J. Li, M. Peng, H. Li, B.-S. Liu, C. Wang, J.-R. Wu, Y.-X. Li, and R. Zeng
Sys-BodyFluid: a systematical database for human body fluid proteome research
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D907 - D912.
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I. Letunic, T. Doerks, and P. Bork
SMART 6: recent updates and new developments
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D229 - D232.
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V. G. Tarcea, T. Weymouth, A. Ade, A. Bookvich, J. Gao, V. Mahavisno, Z. Wright, A. Chapman, M. Jayapandian, A. Ozgur, et al.
Michigan molecular interactions r2: from interacting proteins to pathways
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D642 - D646.
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L. Matthews, G. Gopinath, M. Gillespie, M. Caudy, D. Croft, B. de Bono, P. Garapati, J. Hemish, H. Hermjakob, B. Jassal, et al.
Reactome knowledgebase of human biological pathways and processes
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D619 - D622.
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A. R. Pico, I. V. Smirnov, J. S. Chang, R.-F. Yeh, J. L. Wiemels, J. K. Wiencke, T. Tihan, B. R. Conklin, and M. Wrensch
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D803 - D809.
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G. Chaurasia, S. Malhotra, J. Russ, S. Schnoegl, C. Hanig, E. E. Wanker, and M. E. Futschik
UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D657 - D660.
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M. Shionyu, A. Yamaguchi, K. Shinoda, K.-i. Takahashi, and M. Go
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D305 - D309.
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E. Andres Leon, I. Ezkurdia, B. Garcia, A. Valencia, and D. Juan
EcID. A database for the inference of functional interactions in E. coli
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D629 - D635.
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G. Droc, C. Perin, S. Fromentin, and P. Larmande
OryGenesDB 2008 update: database interoperability for functional genomics of rice
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D992 - D995.
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J. L. Ungerer, B. S. Pratte, and T. Thiel
Regulation of Fructose Transport and Its Effect on Fructose Toxicity in Anabaena spp.
J. Bacteriol., December 15, 2008; 190(24): 8115 - 8125.
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A. E. Vinogradov
Modularity of cellular networks shows general center-periphery polarization
Bioinformatics, December 15, 2008; 24(24): 2814 - 2817.
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