KEGG Pathway Map — Interactive Pathway Network¶
Header: KEGG Pathway Map
The KEGG Pathway Map tab renders an interactive pathway network showing molecular interactions between genes in a selected KEGG pathway, with expression data overlaid as a color gradient.
How It Differs from the KEGG Tab¶
| Feature | KEGG tab | KEGG Pathway Map tab |
|---|---|---|
| Chart type | Horizontal bar chart | Interactive pathway network |
| Visual encoding | Bar length + color | Node color (log2FC gradient) + edge types |
| Gene interactions | No | Yes — all 17 KEGG edge types from KGML |
| Gene-level detail | No | Yes — click any gene for expression info |
| Layout | Static | Zoomable, pannable, switchable layouts |
| Group/complex | No | Yes — protein complexes shown as compound nodes |
| Paralog handling | No | Yes — multiple gene IDs per pathway position |
Controls¶
The contrast is determined by the Contrast dropdown in the sidebar.
| Control | Description |
|---|---|
| Direction | Filter by regulation direction: all, up, or down |
| Select a pathway | Choose which enriched KEGG pathway to visualize |
Pathway Network¶
The interactive network is powered by Cytoscape.js and displays the KEGG pathway layout with your DEG expression data overlaid.
Interactive Features¶
- Zoom & pan — scroll to zoom, drag to pan
- Click a gene — highlights the node and its connected edges, shows an info panel with gene ID, log2FC, padj, direction, and paralog details
- Search — type a gene name in the search box to find and highlight matching nodes
- Layout switcher — switch between KEGG Layout (original coordinates), Force-directed, Grid, or Circle arrangements
- Fit / Reset — re-center the view or reset all highlights
- Legend toggle — show/hide the edge type and node type legend
Node Types¶
| Shape | Color | Meaning |
|---|---|---|
| Rounded rectangle | Red gradient | Up-regulated DEG (intensity = log2FC magnitude) |
| Rounded rectangle | Blue gradient | Down-regulated DEG (intensity = log2FC magnitude) |
| Rounded rectangle | White | DEG with no significant fold change |
| Rounded rectangle | Light green | Pathway gene not in your DEG list |
| Small circle | Light blue | Compound (metabolite) |
| Rounded rectangle | Light purple | Linked pathway |
| Dashed border container | Yellow dashed | Protein complex / group |
Edge Types (KEGG Conventions)¶
Edges represent molecular interactions with styles following KEGG conventions:
| Style | Edge Type | Meaning |
|---|---|---|
| Solid line, triangle arrow | Activation | Direct activation |
| Dashed line, tee arrow | Inhibition | Direct inhibition |
| Solid line, triangle arrow | Expression | Positive transcriptional regulation |
| Dashed line, tee arrow | Repression | Negative transcriptional regulation |
| Dashed line, triangle arrow | Phosphorylation | Post-translational phosphorylation |
| Solid line, no arrow | Binding / Association | Physical binding or complex formation |
| Dashed line, diamond arrow | State Change | Conformational or state modification |
| Dashed line, triangle arrow | Indirect Effect | Indirect causal relationship |
| Solid line, no arrow | Via Compound | Interaction mediated by a compound |
| Solid line, triangle arrow | Reaction | Metabolic reaction (substrate to product) |
Note
The pathway network requires an internet connection to fetch KGML data from the KEGG REST API. The pathway layout preserves the original KEGG coordinate positions for biological accuracy.
Expression Overlay¶
Gene nodes are colored using a blue-white-red gradient based on log2 fold change:
- Blue = strongly down-regulated
- White = near zero fold change
- Red = strongly up-regulated
The color intensity scales relative to the maximum absolute log2FC among matched DEGs.
Group Nodes (Protein Complexes)¶
Genes that function as a complex in the KEGG pathway are grouped inside a dashed container node. The component genes are displayed inside the container, maintaining the biological relationship.
Paralog Handling¶
When a pathway position contains multiple gene IDs (paralogs/isoforms), all are matched against your DEG list. The node displays the paralog with the highest absolute log2FC, and clicking reveals details for all matched paralogs.
Pathway Gene Table¶
An expandable table listing all genes in the selected pathway with their expression data:
- Gene ID, Description, log2FC, padj, Direction
- Summary metrics: up-regulated, down-regulated, and other/missing counts
- CSV download available
Tip
Use the layout switcher to explore pathway structure: KEGG Layout preserves the canonical pathway arrangement, while Force-directed can reveal clusters of interacting genes. Click any gene node to see its expression details and connected interactions.