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KEGG GLYCAN for Integrated Analysis of Pathways, Genes, and Structures

  • Kosuke Hashimoto
  • Minoru Kanehisa

Abstract

While much knowledge about glycans has accumulated, most of the primary data for both experimental and bioinformatics analyses are information on glycan structures and glycan-related genes. Therefore, it is necessary to aggregate all these chemical and genomic information together in an effort to predict complex cellular processes and to understand organism behaviors at a higher level. Following this perspective, we have been developing KEGG (Kyoto Encyclopedia of Genes and Genomes) (Kanehisa et al. 2008) to include three basic glycan resources: (1) GLYCAN, a database of glycan structures; (2) the glycosyltransferase and the glycosidase reaction library; and (3) glycanrelated pathways (Hashimoto et al. 2006). KEGG also includes three useful tools: (4) the Composite Structure Map (CSM), a map illustrating all possible variations in glycan structures within organisms; (5) KegDraw, an intuitive drawing tool for chemical structures; and (6) KCaM, a glycan search and alignment tool (Aoki et al. 2004). All resources are available at KEGG (http://www.genome.jp/kegg/glycan/).

Keywords

Glycan Structure Dynamic Programming Technique Molecular Interaction Network Popup Menu Glycan Biosynthesis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Aoki KF, Yamaguchi A, Ueda N, Akutsu T, Mamitsuka H, Goto S, Kanehisa M (2004) KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res 32:W267–W272PubMedCrossRefGoogle Scholar
  2. Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, Kawasaki T, Kanehisa M (2006) KEGG as a glycome informatics resource. Glycobiology 16:63R–70RPubMedCrossRefGoogle Scholar
  3. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484PubMedCrossRefGoogle Scholar
  4. Kawano S, Hashimoto K, Miyama T, Goto S, Kanehisa M (2005) Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Bioinformatics 21:3976–3982PubMedCrossRefGoogle Scholar
  5. Suga A, Yamanishi Y, Hashimoto K, Goto S, Kanehisa M (2007) An improved scoring scheme for predicting glycan structures from gene expression data. Genome Informatics 18:237–246PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2008

Authors and Affiliations

  • Kosuke Hashimoto
    • 1
  • Minoru Kanehisa
    • 1
  1. 1.Bioinformatics Center, Institute for Chemical ResearchKyoto UniversityUji, KyotoJapan

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