The Kyoto Encyclopedia of Genes and Genomes—KEGG

is organized into three sections: pathway information , genomic information, and computational tools. The pathway information section includes searchable pathway maps and orthologue tables of metabolic and regulatory pathways. There are also extensive catalogues of diseases (human), organisms (completely sequenced genomes or chromosomes), cells (cell lineages), enzymes and`compounds'. All of these are extensively supported by searches of the relevant sections of the KEGG databases, which can be used to help with the correct speci®cation of search terms. The genomic information section is broken down into two parts, gene catalogues and Java map browsers. Thègene catalogues' section is a comprehensive listing of all sequenced genes, for each organism, ordered by species. There are KEGG pages, which have all the genes present in the metabolic and regulatory pathway resources of KEGG, ordered by pathway. There are also links to pages that have the original functionally categorized lists of genes, as de®ned by the relevant sequencing consortia. ThèJava map browsers' section provides genome maps, and a tool that will draw a comparative map between two speci®ed genomes. Currently, the expression map tools only allow users to query the expression data produced using the yeast microarrays. This section will no doubt be expanded as more microarray-based expression analysis is performed. The computational tools section provides BLAST and FASTA searches of the gene and genome catalogues of KEGG. Pathway maps and orthologue tables This section provides metabolic and regulatory pathway maps and tables of orthologous genes, the pathways can also be searched using the tools provided. The metabolic pathway link leads to an ordered table of known metabolic pathways. Clicking on the pathway of interest leads to a ¯ow-chart of thèstandard pathway' (Figure 1), in which all enzymes (Figure 2), substrates, products (Figure 3) and allied pathways are linked to pages on these topics. At the top of the page is an option box for changing to a view of the pathway in a chosen organism. This provides a picture of the pathway in which the enzymes whose genes (or putative functional homo-logues) have been sequenced in that organism are picked out in green. From the pathway page there is also a link to the orthologue table for that pathway, which shows any genes from that pathway that have been clustered to localized areas in the genomes of one or more organisms (Figure 4). Each cluster is denoted by a different background colour in the …