Tutorial:Network Analyzer

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Slideshow Network_Analyzer (about ?? minutes)
Handout Network_Analyzer_Handout.pdf (?? pages)

Tutorial Sources
Tutorial Curators Anna Kuchinsky, Alex Pico


Computation and Visualization of Topological Parameters and Centrality Measures for Biological Networks

Network Analyzer

Biological Use Case: Analyze a biological network and discover its topological properties.

Procedure

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.

Importing Lim 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.

Network Analyzer Network Interpretation

  • 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. Visualize Parameters for Network Analyzer
  • 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.

Extracted components of your network