Gene annotation and pathway mapping in KEGG.

KEGG is a database resource (http://www.genome.jp/kegg/) that provides all knowledge about genomes and their relationships to biological systems such as cells and whole organisms as well as their interactions with the environment. KEGG is categorized in terms of building blocks in the genomic space, known as KEGG GENES, the chemical space, KEGG LIGAND, as well as wiring diagrams of interaction and reaction networks, known as KEGG PATHWAY. A fourth database called KEGG BRITE was also recently incorporated to provide computerized annotations and pathway reconstruction based on the current KEGG knowledgebase. KEGG BRITE contains KEGG Orthology (KO), a classification of ortholog and paralog groups based on highly confident sequence similarity scores, and the reaction classification system for biochemical reaction classification, along with other classifications for compounds and drugs. BRITE is also the basis for the KEGG Automatic Annotation Server (KAAS), which automatically annotates a given set of genes and correspondingly generates pathway maps. This chapter introduces KEGG and its various tools for genomic analyses, focusing on the usage of the KEGG GENES, PATHWAY, and BRITE resources and the KAAS tool (see Note 1).