Multiscale community detection in Cytoscape
Fig 3
Results of hierarchical community detection and downstream analyses.
(A) A hierarchy derived from the BioPlex 2.0 [4] interaction network with OSLOM [25] and annotated by g:Profiler. Red rectangle: a subregion in the hierarchy related to the mediator complex. (B) The menu to set up functional annotation with g:Profiler. (C) A zoom-in view of the sub-hierarchy highlighted in panel A. Red rectangle: a community to be further explored. (D) The interaction subnetwork of the community highlighted in panel C. Proteins, not known as members of the mediator complex, are highlighted (yellow). Related to steps 6–11 in the example workflow. Node color: The overlap (Jaccard Index) between a community and the gene set corresponding to its annotation (panels A and C). Networks can be found on NDEx: http://www.ndexbio.org/#/network/380d5904-bd9f-11ea-aaef-0ac135e8bacf (panel A). http://www.ndexbio.org/#/network/28fdd535-bbe5-11ea-aaef-0ac135e8bacf (panel D).