Cytoscape: Advice on best analysis methods for PPI network
We are working on our first protein interaction network analyses and would like to know if there is a program/plugin available that will spatially arrange (cluster) nodes based on significant GO terms. We have found packages that arrange things in rows or color-code nodes based on GO, but so far it has always then required manual intervention to drag the nodes out into clusters and arrange shared nodes in between, etc. We want to examine some fairly large networks that will likely have several clusters, so it would be really helpful if the clustering was automated and allowed us to choose specific parent/child GO terms to cluster by from a list. Basically, we want to enrich our protein-protein interaction network with the GO terms represented in the network and, instead of looking at all of the GO terms represented, we want to find a way to ‘move up the tree’ to examine the less-specific GO terms to get a general idea of what our proteins of interest are associated with. For example, if we see there is an enrichment of GO terms related to cell division, is there an automated way to visually separate out the nodes in the network after selecting that GO term from a list? Are there any programs or Cytoscape plugins that can do this? We are new to this type of analysis so any advice would be greatly appreciated.
Thanks so much for your help!
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