Ortholog Identifiers for Integration of Genomic and Pathway Information in KEGG

Abstract

KEGG (Kyoto Encyclopedia of Genes and Genomes) [1] is an integrated database system for reconstruction of systemic functional behaviors of the cell, which are represented by networks of interacting molecules, from the complete set of genes in the genome. The KEGG/PATHWAY database contains reference knowledge on the actual networks of interacting molecules in various cellular processes, such as metabolism, membrane transport, signal transduction, cell cycle, and apoptosis. The KEGG/GENES database is a collection of gene catalogs and associated sequence data for all the completely sequenced genomes and some partial genomes including human and mouse. The reconstruction is considered as a process of matching nodes in the two graphs: the reference pathway and the genome. For example, genes in the genome are matched against proteins (enzymes) in the reference metabolic pathway to reconstruct an organism-specific pathway. The automatic reconstruction of metabolic pathways has been successfully implemented in KEGG because the common identifiers, namely the EC numbers, can be utilized for the matching process. We report here the introduction of the ortholog identifiers as an extension of the EC numbers for automatic reconstruction of both metabolic and regulatory pathways.