Cytoscape Nodes/Interactions Export

Question

[mlai2567]

Hi All,

Does anyone with Cytoscape experience know how I might be able to export my network data as a table of nodes and their respective interactions?

I've tried exporting as an SIF but it doesn't seem to include the specific nodes and interactions. Thanks in advance!

Cheers, Michael

Answer 1

[scooter]

Hi Michael, Do you mean export a set of currently selected nodes and their interactions? As you stated, SIF will give you a table of all nodes and their partners. If you want specific nodes and their partners, what I would do is to select the nodes you want to include, select all of the first neighbors of those nodes (Select->Nodes->First neighbors of selected nodes), then create a new, subnetwork of those nodes (File->New Networks->From selected nodes and all edges). Note the "all edges" -- it may be confusing but you'll actually only get the edges that select those nodes. Now you can export that network as a SIF. Does that help?

-- scooter