A global representation of the carbohydrate structures: a tool for the analysis of glycan.
Glycan resources have been developed of late, such as carbohydrate databases, analysis tools, and algorithms for analysis of carbohydrate features. With this background, bioinformatics approaches to carbohydrate research have recently begun using a large amount of protein and carbohydrate data. This paper introduces one of these projects that elucidates the range of carbohydrate structures. In this study, the variety of carbohydrate structures have been enumerated in a global tree structure called variation trees, using the KEGG GLYCAN database, which is a public-domain glycan resource for bioinformatics analysis. Additionally, a glycosyltransferase mapping list of glycosyltransferases and their catalyzing glycosidic linkages was constructed. From this, we present the composite structure map (CSM), which is a structural variation map integrating its variation trees and glycosyltransferase map list. CSM is able to display, for example, expression data of glycosyltransferases in a compact manner, illustrating its versatility as a new bioinformatics resource and tool capable of analyzing carbohydrate structures on a global scale. These resources are available at http://www.genome.jp/kegg/glycan/.
Hashimoto
Kosuke
K
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. khashimo@kuicr.kyoto-u.ac.jp
Kawano
Shin
S
Goto
Susumu
S
Aoki-Kinoshita
Kiyoko F
KF
Kawashima
Masayuki
M
Kanehisa
Minoru
M
D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D002241:Carbohydrates / Q000737:chemistry*; D019295:Computational Biology; D016208:Databases, Factual; D003663:Decision Trees; D006027:Glycosides / Q000737:chemistry; D016695:Glycosyltransferases / Q000737:chemistry; D009005:Monosaccharides / Q000737:chemistry; D011134:Polysaccharides / Q000737:chemistry*
D002241:Carbohydrates; D006027:Glycosides; D009005:Monosaccharides; D011134:Polysaccharides; D016695:Glycosyltransferases