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Question: WGCNA export to cytoscape
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gravatar for 2323982403
6 months ago by
232398240310
232398240310 wrote:

    I'm using the exportNetworkToCytoscape function to export the module of interest to cytoscape. The tutorial first calculate TOM, select node in the network, choosing a threshold of the edge and then export to cytoscape. An edge can exists when the weight between two nodes is above the threshold.

    In cytoscape, I map the degree of nodes to node size, which means that the more connection one node has, the bigger size it will be. The node with big size will be considered hub genes.But the hub genes I selected from the visualization step in cytoscape is completely different from hub genes chosen based on module membership. When I look into the source code of exportNetworkToCytoscape on github, I found it first calculate a dist measure on TOM, and then apply the threshold to the dist measure. I'm wondering if it is logic, because TOM seems to be a measurement of correlation between two nodes,and just filter the edges with low topological overlap is fine, why do we have to calculate the dist of TOM and filter edge on that measure? And why do the hub genes selected from cytoscape is completely different from module membership?

 

ADD COMMENTlink modified 6 months ago by Peter Langfelder1.3k • written 6 months ago by 232398240310
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gravatar for Peter Langfelder
6 months ago by
United States
Peter Langfelder1.3k wrote:

Your reading of the code is incorrect. The code applies as.dist(), not dist(), to the input adjacency matrix (which is usually TOM). as.dist turns a matrix into distance representation by flattening the lower triangle. The information (e.g., numbers) remain exactly the same. 

I'm not so sure about the rest of your question since I rarely use Cytoscape, but in WGCNA hub genes are selected either by calculating the intramodular connectivity from the adjacency (as opposed to TOM), or by ranking genes using their correlation with the module eigengene (kME). Either one should produce results similar to but likely somewhat different from ranking of connectivity calculated from TOM, possibly on a subset of genes.

ADD COMMENTlink modified 6 months ago • written 6 months ago by Peter Langfelder1.3k
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