Cytoscape Edge Filtering
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9.2 years ago
Sudeep ★ 1.6k

Hi, I have a protein protein interaction network overlayed with gene expression data in cytoscape. What I am doing is selecting nodes with interaction data using Cytoscape filter and then Select->Nodes->First Neighbors of Selected Nodes to select nodes with interaction data and its first neighbors. In the resulting sub-network I am also getting edges between the first neighbors, but I want to remove those edges between nodes with no interaction data. Now, is there an easy way (perhaps using filter combinations or some plugins) to do this cytoscape or is the only way to some scripting work ? I am not able to figure this out until now.

Thank you.

cytoscape ppi • 5.8k views
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9.2 years ago
Woa ★ 2.8k

How about this:

  1. Select the node(s) for which u want to select the first neighbours
  2. From Select Menu, Select->edges-> Select adjacent edges
  3. From Select Menu, Select ->Nodes ->First neighbors of selected nodes Now the First neighbours and edges connecting to first neighbours will be selected
  4. Export the selected network as a new network: File ->new ->network -> From Selected Nodes,selected edges
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BTW, did you mean "no expression data" when you said, "between nodes with no interaction data"

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Thank you, it worked, and yes I meant "between nodes with no interaction data" with "no expression data"

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