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SeqUIaSCOPE Documentation

Network Graph

The Network Graph module provides an interactive visualisation of protein-protein interactions within biological pathways, contextualising molecular alterations identified in previous modules. The network is built using interaction data from STRING DB and pathway annotations from KEGG, rendered with Cytoscape.js.

The module consists of two interconnected views: a main graph showing all genes within a selected pathway, and a subgraph showing a focused selection of nodes for detailed analysis.

Graph Elements

Nodes represent genes. They are coloured by log2FC value from the expression data:

  • Red (increasing intensity) — upregulated genes (log2FC > 1)
  • White — no significant change
  • Blue (increasing intensity) — downregulated genes (log2FC < -1)

Node borders are coloured to highlight variants and fusions flagged in previous modules:

  • Toggle Add somatic variants, Add germline variants, or Add fusions using the switches above the main graph to highlight the corresponding genes with distinctive border colours.

Tip: Use variant highlighting to quickly identify genes with actionable mutations within pathway contexts.

Edges represent STRING DB protein-protein interactions. Two display modes are available:

  • Confidence (default) — one edge per gene pair, with edge width reflecting the combined confidence score
  • Evidence — multiple edges per gene pair, one for each type of supporting evidence (experiments, databases, textmining, coexpression, neighborhood, gene fusion, cooccurrence)

Controls

Pathway and Layout

  • Pathway — select a KEGG pathway to display. Only pathways relevant to the patient’s expression data are shown.
  • Layout — choose between cola (recommended for smaller graphs, up to ~100 nodes) and fcose (recommended for large complex networks).
  • Tissue — when multiple reference tissues are available, select which tissue’s log2FC values are used for node colouring.

Edge Filtering

  • Interaction sources — select which types of STRING evidence to include in the network. All sources are selected by default.
  • Interaction score — set a minimum confidence threshold for displayed edges. Available levels: lowest confidence (0.15), medium (0.4, default), high (0.7), highest (0.9). Higher thresholds produce fewer but more reliable interactions.

Tip: Adjusting the confidence threshold significantly changes network density. Start with medium confidence (0.4) and increase if the graph is too dense to interpret.

Graph Manipulation

Three buttons are available below the main graph:

  • Fit graph — adjusts the view to fit all nodes within the visible area. If nodes are selected, fits the selection instead.
  • Clear selection — deselects all selected nodes.
  • Select first neighbors — selects all nodes directly connected to the currently selected node, useful for exploring the local network neighbourhood.

Nodes can be dragged to reposition them. Click a node to select it; click again to deselect.

Subgraph

The subgraph is created automatically when you select one or more nodes in the main graph. It shows the selected nodes and their interactions in an isolated view.

Additional genes can be added to the subgraph by entering gene names in the Add new genes field, even if they are not present in the currently selected pathway. Nodes can be removed from the subgraph using the Remove nodes field. Both the main graph and subgraph share the same edge display settings and confidence thresholds.

Note: When adding genes not present in the original pathway, ensure that gene names are correctly formatted to avoid unrecognised entries.

Data Tables

Both the main graph and the subgraph have associated tables below them showing gene name, log2FC, p-value, pathway name, and number of pathways the gene participates in. Clicking a row in a table highlights the corresponding node in yellow in the graph.