This protocol shows you how to use node grouping functions to manipulate graphs in Cytoscape.
The ability to group nodes together into “metanodes” and collapse them to a single node in a graph is useful for simplifying views of a complex network. The example in this protocol describes application of node grouping functions to data that includes protein-protein interactions and clustered correlations of protein post-translational modifications.
Adapted from Grimes et al., 2018. Sci. Signal. Vol. 11, Issue 531.
First, we will load an example network.
The protein nodes are labeled with their protein symbol, eg CTTN, and nodes representing post-translational modifications are labeled with the protein symbol, type of modification and relevant amino acid, eg CTTN p Y228.
We are going to group all the nodes representing CTTN (Cortactin) and its modifications.
One of the main motivations for creating groups is to be able to simplify the network view by showing only the group nodes. This is done by collapsing groups.
Similarly, collapsed groups can be expanded again to show all the nodes belonging to the group.
A network can have any number of group nodes. For this example network, we can create group nodes for each of the parent proteins by repeating the previous steps for all the proteis (ALK, IRS1, CTNND1, and NPM1):