Nucleic Acids Research, 2004, Vol. 32, Database issue D277-D280
© 2004 Oxford University Press
The KEGG resource for deciphering the genome
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, 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
A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at http://www.genome.ad.jp/kegg/ is the reference knowledge base that integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). These three types of database actually represent three graph objects, called the protein network, the gene universe and the chemical universe. New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database.
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T. Shioda, J. Chesnes, K. R. Coser, L. Zou, J. Hur, K. L. Dean, C. Sonnenschein, A. M. Soto, and K. J. Isselbacher Importance of dosage standardization for interpreting transcriptomal signature profiles: Evidence from studies of xenoestrogens PNAS, August 8, 2006; 103(32): 12033 - 12038. [Abstract] [Full Text] [PDF]
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M. L. Green and P. D. Karp The outcomes of pathway database computations depend on pathway ontology Nucleic Acids Res., August 7, 2006; 34(13): 3687 - 3697. [Abstract] [Full Text] [PDF]
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S. M. Paley and P. D. Karp The Pathway Tools cellular overview diagram and Omics Viewer Nucleic Acids Res., August 7, 2006; 34(13): 3771 - 3778. [Abstract] [Full Text] [PDF]
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K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou, M. van de Guchte, S. Penaud, E. Maguin, M. Hoebeke, P. Bessieres, et al. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system Nucleic Acids Res., July 19, 2006; 34(12): 3533 - 3545. [Abstract] [Full Text] [PDF]
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S. A. Rahman and D. Schomburg Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks Bioinformatics, July 15, 2006; 22(14): 1767 - 1774. [Abstract] [Full Text] [PDF]
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X. Liu, S. Sivaganesan, K. Y. Yeung, J. Guo, R. E. Bumgarner, and M. Medvedovic Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset Bioinformatics, July 15, 2006; 22(14): 1737 - 1744. [Abstract] [Full Text] [PDF]
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M. F. Rudd, G. S. Sellick, E. L. Webb, D. Catovsky, and R. S. Houlston Variants in the ATM-BRCA2-CHEK2 axis predispose to chronic lymphocytic leukemia Blood, July 15, 2006; 108(2): 638 - 644. [Abstract] [Full Text] [PDF]
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I. Lozada-Chavez, S. C. Janga, and J. Collado-Vides Bacterial regulatory networks are extremely flexible in evolution Nucleic Acids Res., July 13, 2006; 34(12): 3434 - 3445. [Abstract] [Full Text] [PDF]
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