Table 2.

Type I error of different methods

Methods	TNFR2 Signaling Pathway (pattern 1)	Fructose and mannose metabolism (pattern 2)	Cytokine-cytokine receptor interaction (pattern 3)
	Type I error (95% CI) P-value	Type I error (95% CI) P-value	Type I error (95% CI) P-value
FPC_AIC	0.060 (0.039,0.081) 0.302	0.058 (0.038,0.078) 0.326	0.054 (0.034,0.074) 0.653
FPC_BIC	0.050 (0.031,0.069) NA	0.048 (0.029,0.067) NA	0.048 (0.029,0.067) NA
FPC_FULL	0.058 (0.038,0.078) 0.492	0.054 (0.034,0.074) 0.673	0.048 (0.029,0.067) 0.932
AML	0.062 (0.041,0.083) 0.346	0.042 (0.024,0.060) 0.653	0.034 (0.018,0.050) 0.285
MSS	0.058 (0.038,0.078) 0.523	0.050 (0.031,0.069) 0.933	0.042 (0.024,0.060) 0.689
RTP_5	0.058 (0.038,0.078) 0.536	0.046 (0.028,0.064) 0.917	0.042 (0.024,0.060) 0.673
RTP_10	0.064 (0.043,0.085) 0.258	0.048 (0.029,0.067) 0.922	0.044 (0.026,0.062) 0.797

For each of the methods, we presented the type I error, the 95% confidence interval of all estimated probabilities, the p-value of McNemar's test for the difference of type I error between FPC_BIC and other methods. The type I error was calculated on the basis of 500 replicates at significance level 0.05.