How can I visualize subset of a network in Cytoscape?

Question

I created a network using separate node and edge files generated from WGCNA. The network has 381 nodes and over 20K edges. I would like to learn how to subset the giant network that zoom in to one gene (node) which is the gene of my interest and other connected nodes that have similar expression to the gene of interest?

Thank you! Abel

I tried to filter based on column value such as weight, but I ended up not getting what I want.

Answer 1

Selecting a particular subset of a large graph containing only nodes 'of interest' is usually straightforward. To answer in detail, we need details of how you define a node of interest.

In general:

• LOOP over nodes
  • IF node is 'interesting'
    • Copy node to subset
• LOOP over every pair of nodes in subset
  • IF node pair is linked in original graph
    • Copy link to subset

I am guessing that you have already tried something like this. If it doesn't work then you may have a bug in your code. We cannot help with that without seeing your code.

Answer 2

In Cytoscape, I'd to this in two steps:

1. Select your starting gene of interest, then select first neighbors (F6), and make subnetwork.
2. Filter your subnetwork based on expression thresholds.