eXamine

eXamine visualizes set-annotated graphs in Cytoscape by overlaying contours of set membership on node-link layouts to support interpretation of enriched gene sets in small biological networks.

Key Features:

• Set-oriented visualization: Overlays contour lines representing set membership directly on node-link graph layouts to show relationships among nodes and sets.
• Enriched gene-set display: Displays enriched gene sets within small biological networks to aid interpretation of gene-level relationships.
• Automation and reproducible workflows: Provides automation features to generate reproducible analysis workflows for consistent visualization outputs.
• Cytoscape integration: Implements these visualization and automation capabilities as an application within the Cytoscape platform.

Scientific Applications:

• Small biological network analysis: Interpretation and visualization of gene set enrichment and relationships within small, set-annotated biological networks.
• Small social-network/community visualization: Visualization of community structures in small social networks by representing set membership over node-link graphs.

Methodology:

Integrating set membership information as contours on a node-link graph layout and providing automated generation of reproducible workflows.