Table 1.

Overview of eight methods.

METHOD	ALGORITHM	TOOL TYPE	REF.	INPUT NETWORK	INPUT EXPRESSION	RUNNING TIME (MIN)
jAM.SA	Simulated annealing	Cytoscape	2	HPRD	Adjusted P-values	∼40
jAM.GR	Greedy search	Cytoscape	28	HPRD	Adjusted P-values	∼4
DEGAS	Greedy heuristic	GUI	29	HPRD	Normalized counts	∼3
BioNet	Integer-Linear Programming	R package	30	HPRD	P-values	∼7
NetBox	Shortest path	Python, Java	31	Preload	Seed genes	∼100
ClustEx	Clustering, shortest path	C & GUI	32	HPRD	Seed genes	∼150
OptDis	Color coding	C	33	HPRD	Normalized counts	∼1560
NetWalker	Random walks	GUI	34	Preload	Adjusted P-values	∼0.1

Notes: jAM.SA denotes jActiveModules using Simulated Annealing; jAM.GR denotes jActiveModules using Greedy Search.