How to Interpret the Values in KEGG Results
The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a comprehensive database encompassing genes, proteins, metabolic pathways, and other biological entities. It is widely utilized in enrichment analyses—such as gene or metabolite enrichment—to facilitate the biological interpretation of experimental datasets.
Following KEGG-based enrichment analysis, the output typically includes several key parameters:
1. Term or ID
Refers to the official name or identifier of the corresponding KEGG pathway.
2. Count
Indicates the number of entries from the input list (e.g., significantly altered genes or metabolites) that are annotated to a specific KEGG pathway.
3. %
Represents the percentage of entries in the input list that are associated with a given KEGG pathway, relative to the total number of input items.
4. P-value
Denotes the probability, as calculated by statistical hypothesis testing, of observing the current level of enrichment (or more extreme) under the assumption of random distribution (null hypothesis). A smaller P-value suggests that the observed enrichment is unlikely to have occurred by chance, thereby indicating a statistically significant association between the input list and the KEGG pathway.
5. Adjusted P-value or Q-value
Represents the P-value corrected for multiple hypothesis testing to control the false discovery rate (FDR). Common correction methods include the Bonferroni and Benjamini-Hochberg procedures. Lower adjusted P-values indicate greater statistical confidence in the association between the input list and a specific KEGG pathway.
6. Enrichment
Describes the magnitude of overrepresentation, typically defined as the ratio between the observed frequency of input items in the pathway and the expected frequency under random distribution. Higher enrichment values suggest a more pronounced and biologically relevant association.
In interpreting KEGG enrichment results, particular attention is usually given to pathways exhibiting low adjusted P-values (e.g., < 0.05) and high enrichment scores, as these are considered to represent biological processes that are significantly perturbed under the given experimental conditions.
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