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Visualizing module eigene relationships in cytoscape

I have used WGCNA to compute signed co-expression gene modules in an RNA data set. I would like to visualize the correlations between the Module Eigengenes (MEs) in a Cytoscape network. I would like to have the modules as nodes and the edges as the correlation between the MEs, specifying the edge thickness and color to indicate the strength and directionality of the ME-ME correlations, respectively. Can someone please advise me on how to accomplish this in Cytoscape? Thank you! Mark Keller

network wgcna cytoscape
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updated by Scooter Scooter • written by MARK • MARK

1 answer

Hi Mark,

I'm not a WGCNA expert, but I know you can import the edge and node files exported as outputs from your WGCNA analysis. Import the edge file first, then import the node file to add all of the data. This should give you your correlation network. There is a good step-by-step discussion here: WGCNA export Network To Cytoscape without trait data, error "Cannot determine node names: nodeNames is NULL and adjMat has no dimnames."

-- scooter

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written by Scooter Scooter

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