Table 2:

Simulation for gene expression data (n, p) = (300, 505). 50 genes have nonzero regression coefficients. 5 clinical covariates are not subject to selection. The gene expressions have AR structure with ρ = 0.5 (upper panel) and ρ = 0.8 (lower panel). mean(sd) of true positives (TP) and false positives (FP) based on 100 replicates.

		LAD_Network	LAD_MCP	LAD_LASSO	Network	MCP	LASSO
AR ρ = 0.5
Error1	TP	44.90(5.65)	40.67(4.59)	38.90(5.19)	40.07(4.70)	28.53(3.92)	48.27(1.20)
	FP	9.77(7.59)	8.63(8.16)	121.93(36.26)	8.13(5.37)	7.67(3.96)	75.57(10.64)
Error2	TP	31.63(13.55)	23.10(9.64)	30.33(6.57)	1.57(2.84)	1.50(2.76)	4.07(6.35)
	FP	14.93(9.85)	56.17(81.31)	103.17(49.89)	3.37(7.73)	3.27(7.94)	11.40(19.09)
Error3	TP	43.68(7.64)	36.28(5.79)	34.88(7.74)	20.03(12.84)	15.42(9.45)	31.83(16.71)
	FP	16.05(29.77)	12.64(20.27)	114.35(57.49)	9.81(6.57)	7.97(5.47)	60.73(33.39)
Error4	TP	39.03(10.15)	31.57(4.70)	34.10(6.26)	11.83(10.91)	9.73(8.51)	20.57(16.26)
	FP	14.33(11.20)	13.50(19.47)	109.87(40.55)	8.93(8.02)	7.67(7.77)	38.83(30.69)
AR ρ = 0.8
Error1	TP	46.93(5.77)	41.00(6.36)	43.70(4.94)	49.60(0.62)	23.93(2.97)	48.27(1.14)
	FP	5.27(6.35)	2.43(2.58)	94.20(38.45)	12.00(8.39)	7.70(5.38)	61.67(15.77)
Error2	TP	43.80(12.34)	23.93(5.46)	38.57(5.9)	10.97(15.16)	4.77(7.68)	9.47(10.68)
	FP	15.07(13.55)	14.20(22.23)	101.42(41.99)	18.50(33.77)	16.07(64.74)	21.82(25.00)
Error3	TP	47.23(7.11)	37.07(5.93)	43.90(4.37)	33.33(20.10)	15.47(10.68)	30.60(18.05)
	FP	4.53(5.06)	11.87(35.83)	91.37(24.94)	27.93(40.69)	19.07(66.48)	49.33(27.36)
Error4	TP	44.37(10.23)	32.30(5.03)	44.30(3.28)	32.57(19.21)	13.63(8.72)	28.27(14.97)
	FP	10.17(9.43)	6.03(8.22)	105.00(32.13)	26.90(20.39)	10.73(6.20)	47.60(26.05)