Comparing distributions of experimental and random diffusion values (p-values for KS tests)
Seeds	Recipients	Randomize Seeds (degree-matched)	Randomize Recipients (degree-matched)	Randomize Seeds (uniform)	Randomize Recipients (uniform)
APOE4_122 Exclusive	APOE_3_156	4.11e-01	3.07e-01	6.31e-01	6.75e-01
APOE_3_156 Exclusive	APOE4_122	3.54e-01	9.25e-01	4.70e-01	5.71e-01
APOE4_122 Exclusive	APOE_3_156 Exclusive	3.04e-01	2.63e-01	7.52e-01	5.10e-01
APOE_3_156 Exclusive	APOE4_122 Exclusive	5.43e-01	9.61e-01	4.70e-01	7.07e-01
APOE4_122 Exclusive	Overlap	8.78e-01	5.27e-01	7.44e-01	6.56e-01
APOE_3_156 Exclusive	Overlap	7.36e-01	6.26e-01	6.90e-01	7.85e-01
Overlap	Exclusives	5.23e-01	8.75e-01	5.46e-02	6.41e-02



Evaluating how well APOE4_122 genes are linked to APOE_3_156 genes, comparing against random

ROC results
Seeds	Recipients	AUROC	Z-score for Random Seeds (degree-matched)	Z-score for Random Recipients (degree-matched)	Z-score for Random Seeds (uniform)	Z-score for Random Recipients (uniform)
APOE4_122 Exclusive	APOE_3_156	0.52	-0.83	-1.01	-0.64	0.64
APOE_3_156 Exclusive	APOE4_122	0.52	-1.74	-0.50	-0.58	0.61
APOE4_122 Exclusive	APOE_3_156 Exclusive	0.51	-1.03	-1.37	-1.10	0.51
APOE_3_156 Exclusive	APOE4_122 Exclusive	0.52	-1.19	-0.14	-0.51	0.65
APOE4_122 Exclusive	Overlap	0.56	0.06	0.57	0.28	0.89
APOE_3_156 Exclusive	Overlap	0.50	-0.93	-0.75	-0.56	-0.03
Overlap	Exclusives	0.54	-0.04	-0.06	0.47	2.22

PRC results
Seeds	Recipients	AUPRC	Z-score for Random Seeds (degree-matched)	Z-score for Random Recipients (degree-matched)	Z-score for Random Seeds (uniform)	Z-score for Random Recipients (uniform)
APOE4_122 Exclusive	APOE_3_156	0.01	-0.40	-0.90	-0.40	0.46
APOE_3_156 Exclusive	APOE4_122	0.01	-1.51	-0.89	-0.52	-0.15
APOE4_122 Exclusive	APOE_3_156 Exclusive	0.01	-0.62	-1.24	-0.65	0.15
APOE_3_156 Exclusive	APOE4_122 Exclusive	0.01	-1.25	-0.56	-0.73	-0.15
APOE4_122 Exclusive	Overlap	0.00	-0.20	-0.13	-0.14	0.08
APOE_3_156 Exclusive	Overlap	0.00	-0.38	-0.79	-0.23	0.07
Overlap	Exclusives	0.01	-0.75	-0.48	-0.19	1.10

Z-scores are computed for the experimental area under ROC or PRC based on distributions of the random areas under these curves
Seeds: Genes where diffusion signal starts FROM)
Recipients: Genes that receive the diffusion signal and that are in the other validated group
Random genes are selected either uniformly or degree matched



Number of genes
**	#Total	# Mapped in the network	Not mapped genes	 
APOE4_122 Exclusive	106	106	
APOE_3_156 Exclusive	140	138	AC093155.3;RFPL2
Overlap	16	16