How do I reduce the network size?

When network is too large, interpretation and visualization become difficult. Some common approaches are provided below:

  • Reduce the input by using larger fold change and/or smaller p value cutoffs before uploading your input lists;
  • Compute the minimum network connecting the seed entities. In filter menu, select “Minimum Network” for shortest path based approach or “Steiner Forest (PCSF)” for Prize-Collecting Steiner Forest approach.
  • Use Degree/Betweenness filter to exclude nodes based on betweenness and degrees.
  • To remove specific nodes and/or edges. In the “Database Selection” page, click the “Browse” button of corresponding interaction network to visualize the network in the browser. Use Advanced Filter options for batch removal of nodes or edges in the new window.
  • To use “Extract Module” function located in the bottom of toolbar to build a subnetwork using an arbitrary list of nodes in the current network.