NORMA

NORMA visualizes and annotates biological networks by integrating precalculated annotations such as Gene Ontology or pathway enrichment and automated community detection to represent and compare network structure and node-level data.

Key Features:

• Network annotation and visualization: Accepts precalculated annotations (e.g., Gene Ontology, pathway enrichment) and represents them on networks using colored pie-chart nodes or color-filled convex hulls.
• Automated community detection: Provides algorithms for automated community detection when pre-existing annotations are not available.
• Layout algorithms and optimization: Implements standard layout algorithms and layout optimization to improve visual separation of annotated groups.
• Group emphasis in visualizations: Provides mechanisms to emphasize specific groups within network visualizations.
• Simultaneous multi-layer encoding: Encodes network topology, communities/annotations, and node categories or expression values concurrently.
• Topological analysis and comparison: Performs basic topological analyses and enables direct comparison of topological features across multiple networks.

Scientific Applications:

• Gene regulatory network analysis: Integration and visualization of gene regulatory networks using Gene Ontology or pathway enrichment annotations.
• Protein–protein interaction and pathway analysis: Representation and annotation of protein-protein interaction networks and metabolic pathways with enrichment results or detected communities.
• Comparative network topology: Comparative analysis of topological features across multiple networks for systems biology studies.

Methodology:

Uses colored pie-chart nodes and color-filled convex hulls for visualization, automated community detection algorithms, standard layout algorithms with layout optimization, and basic topological analyses; accepts precomputed annotations or generates annotations via community detection.