You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/CACvvUxePVTQg_CG1QYWt8nOYLAXhoiE%2B0dc30xsC3AXVzSQNnQ%40mail.gmail.com.
I need to do clustering based on their Gene Ontology biological process inside my network to create some subnetworks of my initial network. In such a way that nodes to be coloured based on their cluster, and each cluster has its own colour. Also, after clustering, I need the layout of the initial network to be kept as before (not merging the nodes in a bigger node), and just each node to be coloured based on their cluster that they belong to. Also, it shows the enriched Gene Ontology biological process of each coloured cluster.
Dear Farah,It's been a while since I've developed the ClusterONE plugin -- I'm glad to see that it still works with Cytoscape and that people are using it for research!ClusterONE is a plugin for clustering networks based on structural information only; the author of your figure probably used some external data source (Gene Ontology maybe?) to get information about the biological processes the proteins belong to, and then assigned meanings to the clusters based on the majority biological process of that cluster; but this is pure guesswork, you need to read the original paper about how the biological process annotations were assigned to the clusters. But one thing is for sure: ClusterONE is not concerned with annotations, it works only with the connections and their weights, so you can use the Gene Ontology annotations and overrepresentation analysis to confirm that a particular cluster found by ClusterONE has biological significance. There are probably other plugins for that in the Cytoscape ecosystem; unfortunately I am not in academia any more and I haven't been following the recent developments so I cannot help you with that.As for the p-value, the ClusterONE plugin provides them in the Results panel of ClusterONE, for each individual cluster; you might need to switch the Results panel to detailed view first; see the documentation:All the best,T.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/422319270.5655928.1607640342217%40mail.yahoo.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/36aa9052-003a-43f3-9ebf-6c667655f2fdn%40googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/e836cc67-8f95-4415-b9aa-1c7092023ae6n%40googlegroups.com.