Fig 1.
Overview of the CDAPS workflow.
A flowchart illustrating various components of the CDAPS framework and the data flow between them. The CD app can send edges of an interaction network for community detection to the CD service. The service then launches the corresponding Docker image which executes the required task and sends back a hierarchy network to the CD app for visualization and community labeling.
Fig 2.
Run community detection on a protein-protein interaction network.
A Cytoscape example screenshot showing the BioPlex 2.0 network [4] imported from NDEx (http://doi.org/10.18119/N91597), along with settings for running OSLOM [25]. Related to steps 4–5 in the example workflow.
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).
Table 1.
Run-time performance of CDAPS.