How Are Highly Enriched Pathways Identified in KEGG Analysis?
The purpose of KEGG pathway analysis is to identify which biological pathways are significantly enriched under your experimental conditions and, consequently, may play a critical role in the biological processes being studied. The following approaches can be used to identify the most highly enriched pathways from the KEGG analysis results:
P-value and Adjusted P-value (e.g., False Discovery Rate - FDR)
The KEGG analysis results generally provide a P-value, which indicates the statistical significance of the enrichment for each pathway. Lower P-values suggest stronger statistical significance.
To account for multiple hypothesis tests, adjusted P-values (such as False Discovery Rate, FDR) are provided to control for Type I errors. A lower adjusted P-value indicates that the pathway is more likely to be truly associated with your experimental conditions.
Enrichment Ratio
The enrichment ratio refers to the ratio of the observed number of genes or proteins in a specific pathway compared to the expected number. A higher enrichment ratio indicates greater enrichment of the pathway in your gene or protein set.
Gene/Protein Count
This refers to the number of differentially expressed genes or proteins observed in a specific pathway. A higher count may suggest a more significant role for that pathway in the biological process under study. However, the overall size of the pathway, such as the total number of genes or proteins it contains, should also be considered.
When reviewing these statistics, look for pathways with low P-values/adjusted P-values, high enrichment ratios, and a high number of differentially expressed genes or proteins. These will be the pathways with the highest enrichment in your analysis.
Additionally, most bioinformatics tools or software display KEGG pathway analysis results in a table format, allowing users to sort the pathways by these parameters, with the most enriched pathways appearing at the top.
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