Table 2.

Performance on the reconstruction of MAPK pathway in comparison with other methods

Method	Directed graph (%)	Undirected graph (%)	P-value
PhosphoChain	77.78	91.18	4.10e-18
PhosphoChain*	56.94	67.65	1.48e-03
MEDUSA	48.61	58.82	2.77e-01
HeR Module	—	52.94	2.23e-01
ADTree	55.56	82.35	1.44e-05
Control	58.33	50.00	—

Note: PhosphoChain* is PhosphoChain trained directly using the PA matrix without the DA matrix. PhosphoChain run with only the MM predicts no MAPK interactions. PhosphoChain produces the same results regardless of whether or not the GRA algorithm (Section 2.3.2) is run.