Table 1.

Features of several methods for identification of altered subnetworks

Feature/Method	heinz	MUFFINN	NetSig	HotNet2	Hierarchical HotNet
Candidate subnetworks	Connected subnetworks	Nearest neighbor subnetworks	Nearest neighbor subnetworks	Unrestricted	Unrestricted
Evaluates statistical significance	No	No	Yes, network permutations	Yes, multiple options	Yes, multiple options
Addresses ascertainment bias in network	No	No	Degree-aware statistical test	Penalizes high-degree nodes	Penalizes high-degree nodes; degree-aware statistical test
Model selection	Yes, on data	No	Yes, on results	No	Yes, on results
Consensus across datasets	No	No	No	Yes	Yes
Supported interaction types	Unweighted and undirected	Weighted and undirected	Unweighted and undirected	Unweighted and undirected	Weighted and directed