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 with 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.

Example - Adding Nodes and Edges with the Knowledge Neighborhood Tool

In this example, we use the Knowledge Neighborhood tool to add edges for protein modifications that are a direct target of the catalytic activity of EGLN family members. Three nodes in the network (cat(p(HGNC:EGLN1)), cat(p(HGNC:EGLN2)), and cat(p(HGNC:EGLN3))) have been selected and the ##Knowledge Neighborhood## window opened through the context menu.

Expand Downstream is selected for the expansion; only edges directed out of the selected nodes are displayed. DIRECTLY_INCREASES is selected for the Edge Relationship. The Target label is filtered for target nodes that contain the string "pmod" in their label.