Querying the KAM and adding Nodes

There are two ways to query a KAM and add selected nodes into your network, either by searching for nodes by function or by searching for nodes via a list of values from a particular BEL namespace.

Add Nodes by function

1. Make sure that a KAM is loaded and available to the KAM Navigator.

2. Select Plugins -> KAM Navigator ->Add KAM Nodes from the main menu. The query window will be displayed.

3. Select a KAM from the list of available KAMs. If a KAM is already available and active it will be already selected in the dropdown list.

4. Select a function type from the Function Type dropdown list and click the Search button. The KAM Navigator will query the KAM and return all KAM Nodes which have a function- return type matching your selection.

   In the example, PROTEIN_ABUNDANCE was selected from the Small Corpus (KAM) network. Note that only the outermost BEL function is used to categorize nodes by function type. For example, PROTEIN_ABUNDANCE includes the nodes p(HGNC:AKT1)and p(HGNC:AKT1, pmod(P, S,473)), but not kin(p(HGNC:AKT1)).

5. (Optional) Apply a secondary filter to the list of KAM Nodes that are returned. This feature is useful to narrow the list of KAM Nodes by namespace identifier (e.g., HGNC) or to node(s) of interest (e.g., AKT). In the example the list of protein abundance nodes was additionally filtered to return only those containing the text string "AKT". As you enter text into the filter, the list of matching KAM Nodes changes.

6. Select an option for expanding the edges associated with the selected nodes in conjunction with adding the selected nodes to the network:

   • All Edges - adds the selected node(s) and all associated edges, both upstream and downstream, along with the connected nodes.
   • Downstream Edges – adds the selected node(s) and edges directed out of the node(s) along with the connected nodes.
   • Upstream Edges – adds the selected node(s) and edges directed into the node(s) along with the connected nodes.
   • Interconnect Nodes – adds the selected node(s) and any edges connecting the selected nodes.
   • None – adds only the selected node(s), with no edges or connected nodes.

7. To finish adding nodes to your network, select one or more nodes from the list and click the Add button. The selected nodes will be added to the Cytoscape network and automatically laid out using a Cytoscape layout algorithm. Depending on the selected edge option, additional nodes and edges upstream and/or downstream from the selected nodes will also be added.

[Examples - Adding Nodes by function] (Add-nodes-by-function---examples)

Add Nodes by a list of identifiers

1. Make sure that a KAM is loaded and available to the KAM Navigator.

2. Select Plugins -> KAM Navigator ->Add KAM Nodes From List from the main menu. The query window will be displayed.

3. Select a KAM from the list of available KAMs. If a KAM is already available and active it will be already selected in the dropdown list.

4. Select a specific function type or ALL from the Function Type dropdown list. The nodes returned in the search will be limited to the selected BEL function.

5. Select a namespace from the Namespace dropdown list. The selected namespace should contain the identifiers from your list.

6. Browse and select a list file using the Browse button.

   Important: The selected file must obey the format specified by the identifier list file format, otherwise the file will fail to load properly

7. After a file is selected click the Search button. The KAM Navigator will query the KAM and return all KAM Nodes found for the identifiers in the file with the selected BEL function type(s).

8. Select an option for expanding the edges associated with the selected nodes in conjunction with adding the selected nodes to the network:

   • All Edges - adds the selected node(s) and all associated edges, both upstream and downstream, along with the connected nodes.
   • Downstream Edges – adds the selected node(s) and edges directed out of the node(s) along with the connected nodes.
   • Upstream Edges – adds the selected node(s) and edges directed into the node(s) along with the connected nodes.
   • Interconnect Nodes – adds the selected node(s) and any edges connecting the selected nodes.
   • None – adds only the selected node(s), with no edges or connected nodes.

9. To finish adding nodes to your network click the Add button. All found nodes will be added to the Cytoscape network and automatically laid out using a Cytoscape layout algorithm. Depending on the selected Expand Edges option, additional nodes and edges upstream and/or downstream from the selected nodes will also be added.

Example - Adding Nodes from a list of identifiers