Table 4. Comparison of active module detection methods with CTD.

Method	Network Structure	Biological Data	Network Propagation Used?	Optimization/Subgraph Search Performed?	Module Assigned Significance?	Permutation testing?
CTD	Gaussian graphical models	Functional -omics	YES	YES	YES	NO
CePa	Pathway Knowledgebases	Gene expression	NO	NO	YES	YES
DEGraph	Pathway Knowledgebases	Gene expression	NO	YES	YES	NO
HotNet/HotNet2	Interaction Knowledgebases	Somatic mutation	YES	YES	YES	YES
MATISSE	Interaction Knowledgebases	Gene expression	NO	YES	NO	NO
Multi-Dendrix	Interaction Knowledgebases	Somatic mutation	NO	YES	YES	YES
NetWalk	Interaction Knowledgebases	Gene expression, RNAi screen	YES	NO	NO*	N/A
PARADIGM	Pathway Knowledgebases	Copy number, Gene expression, Proteomics	YES	NO	YES	YES
PRS	Pathway Knowledgebases	Gene expression	NO	NO	YES	YES
SPIA	Pathway Knowledgebases	Gene expression	NO	NO	YES	YES

* Edge probabilities are computed as Edge Flux scores. The authors state that statistical procedures on this distribution can be applied, but do not offer module significance inherently.