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:
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.
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