KEGG — Pathway Enrichment Analysis

Header: KEGG: Pathway Enrichment Analysis

The KEGG tab presents KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis results, showing which biological pathways are over-represented among your differentially expressed genes. While the GO tab focuses on gene functions, the KEGG tab focuses on broader metabolic and signaling pathways.

Results are loaded from a pre-computed enrichment file (combined_KEGG_enrichment.tsv).

KEGG-Specific Controls

The contrast is determined by the Contrast dropdown in the sidebar — switching the sidebar contrast automatically updates the KEGG report.

Direction

A dropdown to filter by expression direction:

• all — Show pathways enriched across all differentially expressed genes (up + down combined).
• up — Show pathways enriched among upregulated genes only.
• down — Show pathways enriched among downregulated genes only.

The number of displayed pathways is controlled by the Top N slider in the sidebar.

KEGG Enrichment Bar Chart

The main visualization is a horizontal bar chart where each bar represents a KEGG pathway. The x-axis shows the gene count, and bars are colored by statistical significance — with more saturated red indicating more significant enrichment and lighter shades indicating less significant results.

The chart title dynamically reflects your current settings (e.g., "KEGG Enrichment — contrast_name | Top 20 Up + Top 20 Down (p.adjust < 0.05)").

KEGG Enrichment Table (Expandable)

Below the chart, an expandable data table provides the full tabular data including pathway IDs, descriptions, gene ratios, gene counts, p-values, and adjusted p-values.