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Glycobiology Advance Access originally published online on July 13, 2005
Glycobiology 2006 16(5):63R-70R; doi:10.1093/glycob/cwj010
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© The Author 2005. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org

REVIEW

KEGG as a glycome informatics resource

Kosuke Hashimoto2, Susumu Goto2, Shin Kawano2, Kiyoko F. Aoki-Kinoshita2, Nobuhisa Ueda2, Masami Hamajima2, Toshisuke Kawasaki3,4, and Minoru Kanehisa1,2,5

2 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; 3 Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; 4 Research Center for Glycobiotechnology, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; and 5 Human Genome Center, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan

1 To whom correspondence should be addressed; e-mail: kanehisa{at}kuicr.kyoto-u.ac.jp

Bioinformatics approaches to carbohydrate research have recently begun using large amounts of protein and carbohydrate data. In this field called glycome informatics, the foremost necessity is a comprehensive resource for genome-scale bioinformatics analysis of glycan data. Although the accumulation of experimental data may be useful as a reference of biological and biochemical information on carbohydrates, this is insufficient for bioinformatics analysis. Thus, we have developed a glycome informatics resource (http://www.genome.jp/kegg/glycan/) in KEGG (Kyoto Encyclopedia of Genes and Genomes), an integrated knowledge base of protein networks, genomic information, and chemical information. This review describes three noteworthy features: (1) GLYCAN, a database of carbohydrate structures; (2) glycan-related pathways; and (3) Composite Structure Map (CSM), a map illustrating all possible variations of carbohydrate structures within organisms. GLYCAN includes two useful tools: an intuitive drawing tool called KegDraw, and an efficient glycan search and alignment tool called KEGG Carbohydrate Matcher (KCaM). KEGG’s glycan biosynthesis and metabolism pathways, integrating carbohydrate structures, proteins, and reactions, are also a pivotal resource. CSM is constructed as a bridge between carbohydrate functions and structures. CSM is able to display, for example, expression data of glycosyltransferases in a compact manner. In all the KEGG resources, various objects including KEGG pathways, chemical compounds, as well as carbohydrate structures are commonly represented as graphs, which are widely studied and utilized in the computer science field.

Key words: bioinformatics / carbohydrate structure / database / functional genomics / functional glycomics


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