KEGG for taxonomy-based analysis of pathways and genomes

Abstract

KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.

Figure 1.

KEGG is an integrated database containing various biological objects (contents) stored in sixteen databases in four categories. Each object (database entry) is identified by the KEGG identifier (kid) as defined here. Except for GENES and a few other databases, the KEGG identifier takes the form of a prefix followed by a five-digit number. Manually created reference pathway maps, reference Brite hierarchies and reference modules are computationally expanded to organism-specific ones by converting KO identifiers (K numbers) to GENES identifiers in individual organisms (see text).

Figure 2.

Simple URLs, called KEGG weblinks, to retrieve and analyze KEGG objects (database entries). The entry operation retrieves any object specified by the KEGG identifier in the flat-file format. The pathway, brite, module or network operation retrieves a molecular network object specified by the KEGG identifier with optional highlighting of network nodes given in the argument. The genome operation retrieves the genome map of a given organism with optional specification of a gene location. The pathway, brite and genome operations actually launch specialized tools enabling further analysis. In the URL form, www.kegg.jp may be replaced by www.genome.jp for accessing the GenomeNet mirror site.

Figure 3.

The KEGG taxonomy browser, implemented as the Brite hierarchy viewer for taxonomy files, is now linked from the Organism menu of each KEGG pathway map. This example is linked from the lysine biosynthesis pathway map00300, included here by highlighting the plant-specific module M00527, and provides a taxonomy-based global view of organisms and organism groups in which the pathway and associated modules are present.

Figure 4.

The KEGG genome browser is used to display syntenic regions in multiple genomes. Here, a region of eight genes represented as a sequence of eight K numbers is searched against all KEGG organisms. The result of matching organisms is shown in the taxonomy tree, from which selected genomes are displayed by aligning syntenic regions. Color coding is based on the functional category in KEGG.