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)
APOE3_AD_WESr2_median_10random_z3 Exclusive	tier1_31	9.75e-01	8.78e-01	9.88e-01	4.07e-01
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z3	5.43e-02	6.31e-01	7.43e-01	9.72e-01
APOE3_AD_WESr2_median_10random_z3 Exclusive	tier1_31 Exclusive	8.57e-01	8.44e-01	9.37e-01	3.71e-01
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z3 Exclusive	3.81e-02	6.63e-01	8.68e-01	9.84e-01
APOE3_AD_WESr2_median_10random_z3 Exclusive	Overlap	8.32e-01	6.34e-01	5.54e-01	7.33e-01
tier1_31 Exclusive	Overlap	1.98e-02	1.98e-02	1.98e-02	1.98e-02
Overlap	Exclusives	1.23e-06	6.99e-06	1.50e-06	7.97e-07



Evaluating how well APOE3_AD_WESr2_median_10random_z3 genes are linked to tier1_31 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)
APOE3_AD_WESr2_median_10random_z3 Exclusive	tier1_31	0.59	0.08	-0.45	-0.05	1.64
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z3	0.51	-0.97	-0.56	-0.32	0.28
APOE3_AD_WESr2_median_10random_z3 Exclusive	tier1_31 Exclusive	0.58	-0.28	-0.52	-0.06	1.40
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z3 Exclusive	0.50	-1.17	-0.48	-0.56	0.23
APOE3_AD_WESr2_median_10random_z3 Exclusive	Overlap	0.66	0.43	0.68	0.54	0.50
tier1_31 Exclusive	Overlap	1.00	1.87	1.78	2.20	1.77
Overlap	Exclusives	0.61	2.26	3.60	2.38	4.91

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)
APOE3_AD_WESr2_median_10random_z3 Exclusive	tier1_31	0.00	0.10	-0.46	-0.11	0.91
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z3	0.01	0.83	1.15	1.31	0.74
APOE3_AD_WESr2_median_10random_z3 Exclusive	tier1_31 Exclusive	0.00	-0.14	-0.41	0.17	0.08
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z3 Exclusive	0.01	-0.43	-0.02	-0.13	0.13
APOE3_AD_WESr2_median_10random_z3 Exclusive	Overlap	0.00	-0.22	-0.14	-0.18	-0.22
tier1_31 Exclusive	Overlap	0.06	121.58	60.34	488.95	77.35
Overlap	Exclusives	0.03	17.00	33.28	6.22	24.39

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	 
APOE3_AD_WESr2_median_10random_z3 Exclusive	103	101	RFPL2;AC093155.3
tier1_31 Exclusive	30	29	MS4A
Overlap	1	1