Computation and Visualization of Topological Parameters and Centrality Measures for Biological Networks
Biological Use Case: Analyze a biological network and discover its topological properties.
Note: The NetworkAnalyzer plugin now come pre-installed in Cytoscape versions 2.8 and above.
- Go to File>Import>Network from web services and select IntAct Web Service Client under Data Source.
- Search for Lim. When prompted with the results of the search, click Yes to create a network. Enter a name for the network.
- Go to Plugins->Network Analysis->Analyze Network. Decide whether your network should be treated as directed or undirected. In the Lim example, treat the network as undirected.
- Explore the network topology:
- Click on the tabs to see the parameters and their distributions. Parameters are stored as nodes and edge attributes.
- Change the charts (scatter plot/histogram, axes, log scale, colors, zoom...) by clicking chart settings, chart range.
- Fit the function to chart by clicking fit line or fit power law.
- Export the diagrams as graphics by clicking export chart.
- Export data for a spread sheet by clicking export data.
- To visualize topological parameters, click Visualize Parameters. Select Degree for mapping node size, and ClusteringCoefficient for mapping node color.
- Save network statistics by clicking save statistics. Network parameters can be re-imported at any time, and network analysis has to be done only once.
- To make network modifications, click Plugins->Network Modifications->Remove Duplicated Edges or Plugins->Network Modifications->Remove Self-Loops.
- To extract connected components of your network, click Plugins->Network Modifications->Connected Components. Select a connected component of interest to be displayed as a separate network.