network analysis
Definition
Network analysis is a computational approach that examines relationships and interactions between biological entities by representing them as networks of nodes (entities) and edges (connections). In bioinformatics, nodes typically represent genes, proteins, metabolites, or other biomolecules, while edges indicate functional relationships, physical interactions, or regulatory connections. This methodology enables researchers to identify key regulatory hubs, functional modules, pathway crosstalk, and emergent properties that aren't apparent from studying individual components. Network analysis employs graph theory algorithms to calculate centrality measures, detect communities, predict missing interactions, and understand system-level organization in biological systems.
Visualize network analysis in Nodes Bio
Researchers use Nodes Bio to perform network analysis by importing multi-omics datasets and interaction databases, then applying centrality algorithms to identify hub proteins, community detection to reveal functional modules, and path analysis to trace signal propagation. The platform enables interactive exploration of network topology, filtering by connectivity metrics, and overlay of experimental data onto network structures to identify disease-relevant subnetworks.
Visualization Ideas:
- Protein-protein interaction networks colored by centrality scores to highlight regulatory hubs
- Multi-layer networks integrating gene regulation, protein interactions, and metabolic pathways
- Dynamic networks showing temporal changes in connectivity across experimental conditions
Example Use Case
A cancer researcher investigating resistance mechanisms to targeted therapy imports protein-protein interaction data and phosphoproteomics results into a network. Through network analysis, they identify a previously overlooked kinase with high betweenness centrality that bridges two signaling pathways. Community detection reveals this kinase belongs to a tightly connected module of proteins upregulated in resistant cell lines. This hub protein becomes a promising combination therapy target, validated through subsequent knockdown experiments.