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KEGG GLYCAN

Glycome informatics resource integrating genomics and chemistry

KEGG2 PATHWAY BRITE MODULE LIGAND COMPOUND GLYCAN REACTION RMODULE
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KEGG Pathway Maps for Glycans

The KEGG PATHWAY database is a collection of manually drawn KEGG pathway maps representing current knowledge on molecular interaction and reaction networks. Each map is linked to gene information in all completely sequenced genomes, as well as to chemical substance information. The section on: contains metabolic pathway maps for glycans. Some of them contain an alternative representation of glycan biosynthesis or degradation, called the glycan structure map. For example, N-glycan biosynthesis is shown both as a pathway map and a structure map in map00510.

The roles of glycans in various cellular processes may be examined with other pathway maps in the KEGG PATHWAY database, such as:

fig1 N-glycan biosynthesis (pathway map)

fig2 N-glycan biosynthesis (structure map)


Glycans in Cancer Pathways

KEGG Cancer is an interface to various types of cancer information in KEGG. The roles of glycans in cancer pathways are now represented in a KEGG pathway map for: and a BRITE table file for:

Glycosyltransferases

The KEGG Orthology (KO) system is a method to characterize gene/protein functions across organisms. Experimental evidence in specific organisms is extended to other organisms by defining KO groups (or K number entries) in the KEGG ortholog annotation procedure. The K number entries for glycosyltransferases are finely classified ortholog groups distinguishing known substrate specificity, such as K01001 for ALG7. A pathway-based classification [3] is developed as part of the functional hierarchies in the KEGG BRITE database. The classification contains glycosidic linkage information, which may be used to convert gene information to chemical structure information, as is done in the CSM tool described below.

Glycan Binding Proteins

Different types of glycan binding proteins are organized as K number entries and classified as a functional hierarchy of KEGG BRITE.

KEGG GLYCAN Structure Database

The KEGG GLYCAN structure database is a collection of experimentally determined glycan structures [1]. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. Each structure is identified by the G number, such as G00197 for CD65. KEGG GLYCAN is maintained in the KEGG LIGAND relational database. In contrast to the manually drawn KEGG structure maps, the Composite Structure Map (CSM) is computationally generated to represent all possible structures in the KEGG GLYCAN structure database [2]. CSM can be used to examine the structural repertoire inferred from the genomic or transcriptomic repertoire.

KCaM Search Tool

KCaM is a database search program for similar glycan structures [4]. It can be used to search against KEGG GLYCAN or CarbBank. A query glycan structure may be entered with the KegDraw tool.

KegDraw Tool

KegDraw is a standalone Java application for drawing chemical compound structures and glycan structures in a way similar to ChemDraw and ISIS/Draw. KegDraw runs on Mac, Windows, and Linux, and is made freely available to both academic and non-academic users.

References
  1. Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., Kawasaki, T., and Kanehisa, M.; KEGG as a glycome informatics resource. Glycobiology 16, 63R-70R (2006). [pubmed]
  2. Hashimoto, K., Kawano, S., Goto, S., Aoki-Kinoshita, K., Kawashima, M., and Kanehisa, M.; A global representation of the carbohydrate structures: a tool for the analysis of glycan. Genome Informatics 16(1), 214-222 (2005). [pubmed]
  3. Hashimoto, K., Tokimatsu, T., Kawano, S., Yoshizawa, A.C., Okuda, S., Goto, S., and Kanehisa, M.; Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr. Res. 344, 881-887 (2009). [pubmed]
  4. Aoki, K.F., Yamaguchi, A., Ueda, N., Akutsu, T., Mamitsuka, H., Goto, S., and Kanehisa, M.; KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res. 32, W267-W272 (2004). [pubmed]
  5. Kawano, S., Hashimoto, K., Miyama, T., Goto, S., and Kanehisa, M.; Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Bioinformatics 21, 3976-3982 (2005). [pubmed]
  6. Suga, A., Yamanishi, Y., Hashimoto, K., Goto, S., and Kanehisa, M.; An improved scoring scheme for predicting glycan structures from gene expressison data. Genome Informatics 18, 237-246 (2007). [pubmed]

Last updated: March 15, 2013
KEGG GenomeNet Kanehisa Laboratories