- The KEGG (Kyoto Encyclopedia of Genes and Genomes) is a comprehensive, knowledge-based resource that integrates genomic, chemical, and functional information to support the understanding of high-level biological systems.
- Established in 1995 by Minoru Kanehisa and colleagues in Japan, KEGG was designed to systematically link molecular-level information, such as genes and proteins, to cellular processes, pathways, and even organism-level functions. Today, KEGG is one of the most widely used bioinformatics databases for studying biological pathways, molecular interactions, and disease mechanisms.
- At its core, KEGG provides a collection of manually curated pathway maps that represent networks of molecular interactions, reactions, and relations. These pathways cover diverse biological processes, including metabolism, genetic and environmental information processing, cellular processes, organismal systems, human diseases, and drug development. By mapping genes, proteins, and metabolites onto these pathways, researchers can interpret high-throughput omics data—such as transcriptomics, proteomics, or metabolomics—in terms of their functional and systemic context. This makes KEGG a powerful tool for moving from raw data to biological interpretation.
- One of KEGG’s key strengths is its integration of multiple databases under a unified framework. These include KEGG GENES (a collection of gene catalogs for all sequenced organisms), KEGG PATHWAY (curated molecular interaction networks), KEGG MODULE (functional units of pathways), KEGG DISEASE (disease-related information), and KEGG DRUG (drug information and molecular targets). Together, these databases enable researchers to link genomic information to chemical and pharmacological data, facilitating studies in systems biology, pharmacology, and translational medicine.
- KEGG is especially valuable in disease research, as it provides curated pathway maps for numerous human diseases, such as cancer, diabetes, and neurodegenerative disorders. These maps highlight how disruptions in molecular pathways contribute to disease mechanisms, offering insights into potential therapeutic strategies. Furthermore, KEGG DRUG and KEGG DISEASE serve as important resources for drug discovery and precision medicine by linking compounds to their targets and associated pathways.
- The KEGG database is accessed primarily through its web interface, which provides interactive tools for browsing, searching, and mapping user-submitted data onto KEGG pathways. Many bioinformatics pipelines and software tools (such as DAVID, GSEA, and clusterProfiler) incorporate KEGG for functional enrichment analysis, where sets of genes or proteins are tested for overrepresentation in specific pathways. This makes KEGG a standard resource in omics data interpretation and pathway-based systems biology studies.
- In summary, KEGG is a foundational bioinformatics resource that integrates genomic, chemical, and functional data to map biological systems and disease processes. Its curated pathway maps, comprehensive database structure, and wide applicability in omics data analysis make it indispensable for researchers aiming to bridge molecular data with higher-order biological insights. By linking genes, proteins, and metabolites to pathways, KEGG provides a powerful framework for understanding cellular organization, disease mechanisms, and therapeutic opportunities.
