Table 1.

The four pathway reconstruction methods and the parameters (in bold) tuned for each.

Algorithm	Description	Parameters and default values	Range tested
PathLinker9	Connects receptors to transcriptional regulators via weighted k-shortest paths.	k (default = 100): number of shortest paths	1–1000
NetBox10	Hierarchically constructs network using hypergeometric test.	p (default = 0.05): p value threshold for adding an edge	0–1
Prize-Collecting Steiner Forest6,42	Assigns prizes to nodes and costs to edges; solves for highest scoring subnetwork with message-passing algorithm.	β (default = 1): relative weight of the node prizes versus edge costs	0–5
		ω (default = 6): cost of adding an additional tree to the solution network	0–10
		μ (default = 0): degree penalty	0–1
Minimum-cost flow12	Assigns edges costs and nodes as sources and targets of flow. Finds the network that satisfies flow constraints for the least cost.	f (default = 10): amount of flow pushed through the network from sources to targets	1–50
		c (default = 1): edge flow capacity	1–25