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Nucleic Acids Research 2006 34(Database Issue):D354-D357; doi:10.1093/nar/gkj102
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Nucleic Acids Research, 2006, Vol. 34, Database issue D354-D357
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

From genomics to chemical genomics: new developments in KEGG

Minoru Kanehisa1,2,*, Susumu Goto1, Masahiro Hattori1, Kiyoko F. Aoki-Kinoshita1, Masumi Itoh1, Shuichi Kawashima2, Toshiaki Katayama2, Michihiro Araki2 and Mika Hirakawa1,3

1Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611-0011, Japan 2Human Genome Center, Institute of Medical Science, University of Tokyo Minato-ku, Tokyo 108-8639, Japan 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 14, 2005. Revised October 17, 2005. Accepted October 17, 2005.

The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules. Specifically, RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps.


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Regulation of Glycan Structures in Animal Tissues: TRANSCRIPT PROFILING OF GLYCAN-RELATED GENES
J. Biol. Chem., June 20, 2008; 283(25): 17298 - 17313.
[Abstract] [Full Text] [PDF]

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 Cancer Epidemiol. Biomarkers Prev.Home page
J. S. Chang, R.-F. Yeh, J. K. Wiencke, J. L. Wiemels, I. Smirnov, A. R. Pico, T. Tihan, J. Patoka, R. Miike, J. D. Sison, et al.
Pathway Analysis of Single-Nucleotide Polymorphisms Potentially Associated with Glioblastoma Multiforme Susceptibility Using Random Forests
Cancer Epidemiol. Biomarkers Prev., June 1, 2008; 17(6): 1368 - 1373.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
S. Gotz, J. M. Garcia-Gomez, J. Terol, T. D. Williams, S. H. Nagaraj, M. J. Nueda, M. Robles, M. Talon, J. Dopazo, and A. Conesa
High-throughput functional annotation and data mining with the Blast2GO suite
Nucleic Acids Res., June 1, 2008; 36(10): 3420 - 3435.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
L. Smeenk, S. J. van Heeringen, M. Koeppel, M. A. van Driel, S. J. J. Bartels, R. C. Akkers, S. Denissov, H. G. Stunnenberg, and M. Lohrum
Characterization of genome-wide p53-binding sites upon stress response
Nucleic Acids Res., June 1, 2008; 36(11): 3639 - 3654.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
D. Aguilar, L. Skrabanek, S. S. Gross, B. Oliva, and F. Campagne
Beyond tissueInfo: functional prediction using tissue expression profile similarity searches
Nucleic Acids Res., June 1, 2008; 36(11): 3728 - 3737.
[Abstract] [Full Text] [PDF]

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 Hum Mol GenetHome page
A. S. Chen-Plotkin, F. Geser, J. B. Plotkin, C. M. Clark, L. K. Kwong, W. Yuan, M. Grossman, V. M. Van Deerlin, J. Q. Trojanowski, and V. M.-Y. Lee
Variations in the progranulin gene affect global gene expression in frontotemporal lobar degeneration
Hum. Mol. Genet., May 15, 2008; 17(10): 1349 - 1362.
[Abstract] [Full Text] [PDF]

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 Infect. Immun.Home page
F. Galka, S. N. Wai, H. Kusch, S. Engelmann, M. Hecker, B. Schmeck, S. Hippenstiel, B. E. Uhlin, and M. Steinert
Proteomic Characterization of the Whole Secretome of Legionella pneumophila and Functional Analysis of Outer Membrane Vesicles
Infect. Immun., May 1, 2008; 76(5): 1825 - 1836.
[Abstract] [Full Text] [PDF]

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 GeneticsHome page
P. May, S. Wienkoop, S. Kempa, B. Usadel, N. Christian, J. Rupprecht, J. Weiss, L. Recuenco-Munoz, O. Ebenhoh, W. Weckwerth, et al.
Metabolomics- and Proteomics-Assisted Genome Annotation and Analysis of the Draft Metabolic Network of Chlamydomonas reinhardtii
Genetics, May 1, 2008; 179(1): 157 - 166.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
K. Horan, C. Jang, J. Bailey-Serres, R. Mittler, C. Shelton, J. F. Harper, J.-K. Zhu, J. C. Cushman, M. Gollery, and T. Girke
Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis
Plant Physiology, May 1, 2008; 147(1): 41 - 57.
[Abstract] [Full Text] [PDF]

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 Cancer Res.Home page
A. Jimeno, A. C. Tan, J. Coffa, N.V. Rajeshkumar, P. Kulesza, B. Rubio-Viqueira, J. Wheelhouse, B. Diosdado, W. A. Messersmith, C. Iacobuzio-Donahue, et al.
Coordinated Epidermal Growth Factor Receptor Pathway Gene Overexpression Predicts Epidermal Growth Factor Receptor Inhibitor Sensitivity in Pancreatic Cancer
Cancer Res., April 15, 2008; 68(8): 2841 - 2849.
[Abstract] [Full Text] [PDF]

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 J. Bacteriol.Home page
M. A. Oberhardt, J. Puchalka, K. E. Fryer, V. A. P. Martins dos Santos, and J. A. Papin
Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1
J. Bacteriol., April 15, 2008; 190(8): 2790 - 2803.
[Abstract] [Full Text] [PDF]

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 MicrobiologyHome page
J. Hegermann, S. Halbedel, R. Dumke, J. Regula, R. R. Gabdoulline, F. Mayer, J. Stulke, and R. Herrmann
The acidic, glutamine-rich Mpn474 protein of Mycoplasma pneumoniae is surface exposed and covers the complete cell
Microbiology, April 1, 2008; 154(4): 1185 - 1192.
[Abstract] [Full Text] [PDF]


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