Kyoto encyclopedia of genes and genomes (KEGG)

Kyoto encyclopedia of genes and genomes (KEGG) integrates curated databases and computational methods to map genes, molecules, and biochemical reactions onto pathways and molecular networks for interpretation of genomic and high-throughput data.

Key Features:

• Comprehensive Databases: The GENES database contains gene catalogs for completely sequenced and selected partial genomes with functional annotations; the PATHWAY database provides diagrams of metabolic and regulatory pathways plus ortholog group tables summarizing conserved subpathways (motifs); and the LIGAND database documents chemical compounds, enzyme molecules, and enzymatic reactions.
• KEGG Atlas: A single comprehensive global map covers approximately 120 KEGG metabolic pathway maps and 10 BRITE hierarchies and supports mapping of high-throughput experimental data onto the global pathway map.
• Computational Tools: Tools include reconstruction of biochemical pathways from complete genome sequences, predictive models for gene regulatory networks from gene expression profiles, and Java graphics tools for browsing and comparing genome maps and manipulating expression maps.
• KEGG Mapping and NETWORK: KEGG Mapping reconstructs molecular network systems using the concept of functional orthologs and integrates pathway maps with network variation maps in the KEGG NETWORK database to associate diseases with perturbed molecular networks caused by gene variants, pathogens, and environmental factors.
• Integration with MODULE and KO: KEGG links to the MODULE database of conserved functional units and the KO (KEGG Orthology) database of functional orthologs, including expanded virus KOs to support analysis of virus–cell interactions.

Scientific Applications:

• Genomic Interpretation: Provides a framework to interpret genome sequences in the context of cellular processes and pathway membership.
• Pathway Analysis: Enables analysis and visualization of metabolic and regulatory pathways, including organism-specific pathway reconstruction via orthologs.
• Disease Research: Associates network variants with diseases to support investigation of molecular mechanisms driven by gene variants, pathogens, or environmental factors.
• High-throughput Data Integration: Supports mapping and integration of large-scale datasets such as gene expression profiles onto pathways and network maps.

Methodology:

Reconstruction of biochemical pathways from complete genome sequences; predictive modeling of gene regulatory networks from gene expression profiles; KEGG Mapping using functional orthologs and integration of pathway maps with network variation maps in the KEGG NETWORK database; and use of Java-based graphics tools for genome map comparison and expression map manipulation.