NAP

NAP performs topological analysis and comparative profiling of biological networks to identify key nodes, edges, and structural similarities and differences between networks.

Key Features:

• Topological Feature Exploration: Computes and analyzes network topological features to characterize network structure and dynamics.
• Node and Edge Ranking: Ranks nodes and edges based on topological properties to identify key network components.
• Inter- and Intra-Network Comparison: Performs simultaneous comparisons of topological features across different networks to identify similarities, differences, and intersections.
• Profile Comparisons and Intersection Analysis: Compares network profiles and identifies intersections between profiles across networks.
• Visualization Capabilities: Generates simplified plots of topological characteristics within the same network for interpretability.
• Versatility in Network Types: Supports medium-scale networks including weighted and unweighted, directed and undirected, and bipartite graphs.

Scientific Applications:

• Systems Biology: Applied to gene expression, signal transduction, protein interaction, and biomedical literature co-occurrence networks to profile and compare network structures.
• Comparative Genomics and Proteomics: Identifies shared and distinct network components across datasets to support comparative analyses.

Methodology:

Implemented in R and using the igraph library for network analysis and visualization.