Question: Cytoscape Edge Filtering
gravatar for Sudeep
7.5 years ago by
Sudeep1.6k wrote:

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.

ppi cytoscape • 4.7k views
ADD COMMENTlink written 7.5 years ago by Sudeep1.6k
gravatar for Woa
7.5 years ago by
United States
Woa2.7k wrote:

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
ADD COMMENTlink written 7.5 years ago by Woa2.7k

BTW, did you mean "no expression data" when you said, "between nodes with no interaction data"

ADD REPLYlink written 7.5 years ago by Woa2.7k

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

ADD REPLYlink written 7.4 years ago by Sudeep1.6k
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