Loading Network

  • Start Cytoscape and download the demo network.
  • Open the demo network using File → Open...
  • When the network first opens, the entire network is not visible because of the default zoom factor used. To see the whole network, we can use the View → Fit Content function.

Filter Interactions

  • Your network contains a combination of protein-protein (pp) and protein-DNA (pd) interactions. Next, we will filter out the protein-protein interactions to focus on the protein-DNA interactions.
  • First, let's select all protein-protein interactions.
    • Go to the Select tab in the Cytoscape Control Panel (the leftmost panel).
    • Click on the + and create a Column Filter.
    • Click on Choose column... and select Edge: interaction
    • Now in the text field enter pp. This will select all of the edges with the protein-protein interactions.
  • You should now see many edges in the network selected (i.e., colored red).
  • Since we're only interested in the protein-DNA edges, we can delete the protein-protein edges we've just selected.
  • To delete selected nodes or edges, you can just hit the DELETE key or use the menu Edit → Delete Selected Nodes and Edges
  • You should now see many unconnected nodes in the network.
  • Now, lets clean up the network by applying a force-directed layout under Layout → Prefuse Force Directed Layout.
  • The largest component of the final filtered and cleaned up network should look like this:

Observe the Network

  • Notice that three dark red (highly induced) nodes are in the same region of the graph.
  • Notice that there are two nodes that interact with all three red nodes: GAL4 (YPL248C) and GAL11 (YOL051W).
  • Let's select these two nodes and their immediate neighbors.
    • First select GAL4 (YPL248C) by clicking on it.
    • Now, extend the selection by holding down the shift key and clicking on GAL11 (YOL051W).
    • Finally, select their neighbors by control-6 (or ⌘-6 on a Mac), or by the menu Select → Nodes → First Neighbors of Selected Nodes → Undirected
  • It is sometimes useful to create a new network from selected nodes.
    • Create a new network by selecting File → New → Network → Selected nodes, all edges.
      • (Even though we say all edges, only the edges connecting the selected nodes will actually be used.)
    • As before, we may need to do a View → Fit Content.

With some layout and zooming, this new network should appear similar to the one shown: