KEGG
Introduction
The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a comprehensive bioinformatics resource that provides a suite of databases and associated software tools for understanding high-level functions and utilities of biological systems. These systems include the cell, the organism, and the ecosystem, all derived from genomic and molecular-level information. KEGG is widely used in the fields of genomics, proteomics, metabolomics, and other areas of systems biology. It is particularly renowned for its pathway maps, which integrate genomic, chemical, and systemic functional information.
History and Development
KEGG was initiated in 1995 by Minoru Kanehisa, a professor at the Institute for Chemical Research, Kyoto University. The project was conceived as a part of the Japanese Human Genome Program, with the aim of providing a computational resource for understanding biological systems. Over the years, KEGG has evolved significantly, expanding its databases and tools to accommodate the growing complexity and volume of biological data. The project is maintained by the Kanehisa Laboratories, with ongoing contributions from researchers worldwide.
Database Structure
KEGG is organized into several interconnected databases, each serving a specific purpose:
KEGG PATHWAY
KEGG PATHWAY is perhaps the most well-known component of KEGG. It contains pathway maps that represent molecular interaction and reaction networks. These maps cover a wide range of biological processes, including metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems, and human diseases. Each pathway map is a manually curated collection of pathway diagrams that integrate information from various sources.
KEGG GENES
KEGG GENES is a database of gene catalogs for all sequenced organisms. It provides a comprehensive collection of gene sequences and annotations, linking them to their corresponding pathways and functional modules. This database is crucial for comparative genomics and functional genomics studies.
KEGG ORTHOLOGY
The KEGG ORTHOLOGY (KO) system is a classification of orthologous genes across different species. It is used to infer functional annotations and to predict gene functions in newly sequenced genomes. The KO system is essential for understanding the evolutionary relationships between genes and their associated functions.
KEGG MODULE
KEGG MODULE is a collection of functional units, or modules, that represent specific biological functions. These modules are defined based on the KEGG PATHWAY and KEGG ORTHOLOGY databases and are used to analyze and interpret genomic and metagenomic data.
KEGG REACTION
KEGG REACTION is a database of enzymatic reactions, providing detailed information about the chemical transformations that occur in biological systems. It is linked to the KEGG PATHWAY and KEGG COMPOUND databases, facilitating the study of metabolic networks and enzyme functions.
KEGG COMPOUND
KEGG COMPOUND is a database of chemical substances, including metabolites, drugs, and other small molecules. It provides information about the chemical structures, properties, and interactions of these compounds, linking them to their corresponding pathways and reactions.
KEGG DRUG
KEGG DRUG is a database of approved drugs and their targets. It provides information about the chemical structures, mechanisms of action, and therapeutic uses of drugs, linking them to their corresponding pathways and diseases.
KEGG DISEASE
KEGG DISEASE is a database of human diseases, providing information about the genetic and molecular basis of diseases. It links diseases to their associated pathways, genes, and drugs, facilitating the study of disease mechanisms and drug discovery.
Applications of KEGG
KEGG is widely used in various fields of biological research and has numerous applications:
Genomics and Proteomics
In genomics and proteomics, KEGG is used to annotate and analyze gene and protein functions. By linking genes and proteins to their corresponding pathways, researchers can gain insights into the biological roles and interactions of these molecules.
Metabolomics
In metabolomics, KEGG is used to study metabolic pathways and networks. By analyzing the chemical transformations and interactions in metabolic pathways, researchers can understand the metabolic profiles and dynamics of organisms.
Drug Discovery
KEGG is a valuable resource for drug discovery, providing information about drug targets, mechanisms of action, and therapeutic uses. By linking drugs to their corresponding pathways and diseases, researchers can identify potential drug candidates and therapeutic strategies.
Systems Biology
In systems biology, KEGG is used to model and simulate biological systems. By integrating genomic, chemical, and systemic functional information, researchers can construct computational models of biological processes and predict their behaviors.
KEGG Tools
KEGG provides a suite of computational tools for analyzing and interpreting biological data:
KEGG Mapper
KEGG Mapper is a collection of tools for mapping and analyzing genomic and chemical data. It includes tools for pathway mapping, module mapping, and reaction mapping, allowing researchers to visualize and interpret their data in the context of KEGG pathways.
KEGG REST API
The KEGG REST API is a web service that provides programmatic access to KEGG databases and tools. It allows researchers to retrieve and analyze KEGG data using custom scripts and applications.
KEGG Atlas
KEGG Atlas is an interactive viewer for exploring KEGG pathway maps. It provides a graphical interface for navigating and visualizing pathways, allowing researchers to explore the complex networks of molecular interactions.
Future Directions
The KEGG project continues to evolve, with ongoing efforts to expand and update its databases and tools. Future directions for KEGG include the integration of new types of data, such as epigenomic and transcriptomic data, and the development of new computational tools for systems biology research. As the volume and complexity of biological data continue to grow, KEGG will remain an essential resource for understanding the functions and utilities of biological systems.