Chapter 9 - KEGG GLYCAN for Integrated Analysis of Pathways, Genes, and Glycan Structures

Abstract

This chapter focuses on the Kyoto Encyclopedia of Genes and Genomes (KEGG) approach for integration of glycomics databases.KEGG is an integrated knowledge base for understanding higher-level functions of cellular processes and organism behaviors. The KEGG GLYCAN resource for glycomics research is organized according to the three perspectives of genomic, chemical, and systemic functional information. Rapid improvements in sequencing techniques allow the determination of a variety of genome sequences. Genomic information enables the pathway map and the structure map to represent systemic differences in organisms. The process of how newly determined genomes are integrated into the database and how the data connections are constructed is described. All protein sequences can be obtained directly from the genome sequence once a proper gene model is determined. The KEGG pathway is a collection of manually drawn pathway maps representing molecular interaction networks, including metabolic pathways, regulatory pathways, molecular complexes, and structural relationships. In contrast to the high-throughput and high-quality sequence data for nucleic acids and proteins, glycan structures with full linkage information are low-throughput data. Glycan structures in a cell, such as the genome and the transcriptome, cannot be comprehensively elucidated because of the difficulties in determining the types of glycosidic linkages. The structures may be obtained indirectly from the genome sequence through our knowledge on biosynthetic pathways and enzymes.