Bioinformatics database · BEGINNER LESSON
KEGG
KEGG is a manually curated database resource that links genes, proteins, chemicals, pathways, and disease information for biological interpretation. It uses standardized identifiers and pathway maps to connect genome data to higher-level biological functions.
What KEGG is
KEGG, short for Kyoto Encyclopedia of Genes and Genomes, is a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. It is manually curated, meaning people build and maintain it from published literature and expert knowledge rather than by automatic learning alone. KEGG organizes biological objects into systems, genomic, chemical, and health information. [0,1,2]
[1] KEGG for taxonomy-based analysis of pathways and genomes [2] Toward understanding the origin and evolution of cellular organisms [3] KEGG: Kyoto Encyclopedia of Genes and Genomes - PMC
What it measures and stores
KEGG does not measure a single lab variable. Instead, it stores connected biological information: genes and proteins, small molecules and reactions, pathway maps, BRITE hierarchies, modules, genomes, and disease-related network elements. Each object has a KEGG identifier, often written as a prefix plus a five-digit number. [0,1,2]
[1] KEGG for taxonomy-based analysis of pathways and genomes [2] Toward understanding the origin and evolution of cellular organisms [3] KEGG: Kyoto Encyclopedia of Genes and Genomes - PMC
How it works
KEGG uses pathway maps as molecular wiring diagrams. In these maps, rectangles usually represent gene products, mostly proteins, and circles represent other molecules, mostly chemical compounds. Arrows show interactions or reactions. KEGG also uses KO, which stands for KEGG Orthology, to group functional orthologs: genes in different organisms that play the same role in a molecular network. That allows reference maps to be expanded into organism-specific maps by replacing KO identifiers with genes from a chosen organism. [0,1,2]
[1] KEGG for taxonomy-based analysis of pathways and genomes [2] Toward understanding the origin and evolution of cellular organisms [3] KEGG: Kyoto Encyclopedia of Genes and Genomes - PMC
Why it is useful
By connecting genome information with molecular networks, KEGG helps researchers infer cell and organism functions from sequence data. It is used to compare conserved functional links among organisms and to interpret hidden features in genome and metagenome sequences. This makes it useful for systematic analysis of gene functions and for reconstructing biological systems from genome information. [0,1,2]
[1] KEGG for taxonomy-based analysis of pathways and genomes [2] Toward understanding the origin and evolution of cellular organisms [3] KEGG: Kyoto Encyclopedia of Genes and Genomes - PMC
Limits and careful interpretation
KEGG is a curated reference resource, not a complete direct measurement of every cell state. Its maps are simplified diagrams, so they summarize known relationships rather than show every detail of a living system. Some parts are built from human expert judgment, and the organism-specific view depends on how genes are assigned to KO groups. [0,1,2]
[1] KEGG for taxonomy-based analysis of pathways and genomes [2] Toward understanding the origin and evolution of cellular organisms [3] KEGG: Kyoto Encyclopedia of Genes and Genomes - PMC
SEE THE IDEA
How KEGG connects genome data to biological meaning
Sequenced genes and proteins from an organism
Genes are grouped by functional orthologs
A diagram of molecular interactions and reactions
Functions inferred from the organized network
Genome data are annotated with KO groups, which are placed onto pathway maps to infer functions.
KEGG uses standardized groups and diagrams to turn sequence information into interpretable biological networks.
TRY IT YOURSELF
Test your understanding
Choose an answer, then check the explanation.
PUT IT TOGETHER
Match each concept to its meaning
Drag a label onto its description, or select a label and then select a description. This also works with a keyboard.
4 pairs to match
Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.