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Nucleic Acids Research Advance Access published online on October 30, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp896
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

KEGG for representation and analysis of molecular networks involving diseases and drugs

Minoru Kanehisa1,2,*, Susumu Goto1, Miho Furumichi1,3, Mao Tanabe1,3 and Mika Hirakawa1,3

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 10, 2009. Revised October 4, 2009. Accepted October 6, 2009.

Most human diseases are complex multi-factorial diseases resulting from the combination of various genetic and environmental factors. In the KEGG database resource (http://www.genome.jp/kegg/), diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. Disease information is computerized in two forms: pathway maps and gene/molecule lists. The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. This database also captures knowledge about two types of molecular networks: the interaction network with target molecules, metabolizing enzymes, other drugs, etc. and the chemical structure transformation network in the history of drug development. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.


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