cytoscape subnetwork from WGCNA based modules

Question

[Omics data mining]

Hello

I have identified modules linked to some traits of interest in our study. All modules were imported in cytoscape. As next step, I want to predict subnetwork using TieDie ( one of the cytoscape App). One of the network consist of 102 edges and 306 nodes. After running, TieDie on that network, I am getting same 102 edges and 306 nodes , indicates no subnetwork was created.

If anyone has experience how to use it, Please help me here to fix this.

I will aprreaciate all the suggestions

Thanks

Answer 1

[Kevin Blighe]

You must mean this: TieDIE - Tied Diffusion Through Interacting Events

You should try altering the parameters for TieDie and / or for WGCNA. Your network may already statistically be a sub-network itself. You could try a larger network size as input to TieDie.

Finally, there are other Cytoscape plugins that can identify sub-networks ('modules')

• https://apps.cytoscape.org/apps/subnetworkcreator
• https://apps.cytoscape.org/apps/with_tag/functionalmoduledetection:

Kevin