Cytoscape network analysis

Question

[Marco Pannone]

Hey everybody

After performing GSEA, I have selected some genes of interest from different dysregulated pathways and I am now trying to perform network visualization in Cytoscape using them as input.

After displaying my network, clearly now all the proteins from the different pathways get combined into one single "a bit messy" network. I would like to find a way for keeping still all of them in the same network but splitting the nodes accordingly to the pathway they belong to.

This way I can keep a cleaner layout identifying the different pathways of interest but still visualizing interactions among nodes of each one.

An example of what I mean is represented in this picture:

Thanks in advance for your help!

Answer 1

[Soheil]

You can first use the EnrichmentMap plugin to create your network. Then you can use the AutoAnnotate plugin for clustering and annotating your network. See this paper for further details: Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

[Marco Pannone]

Thanks for the suggestion, I will have a look!