Navigating a KAM

Once you have one or more KAM Nodes and edges loaded into a Cytoscape network you can add additional nodes and edges via the Add KAM Nodes menu or by expanding one or more of the nodes that are already in your network view with adjacent nodes and/or edges from the KAM (the Knowledge Neighborhood).

To explore the Knowledge Neighborhood of selected node(s):

1. Select one or more KAM Nodes from the Network View.

2. Right-click to show the context menu. Options are:

   • Expand Downstream - adds all KAM edges directed out of the selected node(s) along with the connected nodes.
   • Expand Upstream - adds all KAM edges directed into the selected node(s) along with the connected nodes.
   • Expand Downstream & Upstream - adds all KAM edges associated with the selected node(s), along with the connected nodes.
   • Interconnect - adds all edges connecting the selected nodes. At least two nodes must be selected.
   • Knowledge Neighborhood - opens a dialog window that allows you to filter and select specific edges adjacent to the selected node(s).

Example - Adding Nodes and Edges using ##Expand Upstream

In this example, Expand Upstream was selected to add the nodes and edges upstream from the biological process node bp(GO:apoptosis) to the network.