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)
FCS_3ea_AD_142 Exclusive	TIER1_GS	1.18e-14	1.46e-13	1.19e-17	6.09e-16
TIER1_GS Exclusive	FCS_3ea_AD_142	1.42e-03	3.40e-04	4.64e-07	9.42e-11
FCS_3ea_AD_142 Exclusive	TIER1_GS Exclusive	1.33e-09	4.48e-10	2.68e-14	8.58e-12
TIER1_GS Exclusive	FCS_3ea_AD_142 Exclusive	1.62e-02	2.84e-03	4.64e-06	1.27e-09
FCS_3ea_AD_142 Exclusive	Overlap	2.98e-14	5.39e-05	2.98e-14	8.35e-13
TIER1_GS Exclusive	Overlap	1.38e-11	1.16e-09	2.98e-14	3.69e-10
Overlap	Exclusives	1.77e-09	1.07e-11	1.22e-23	2.39e-18



Evaluating how well FCS_3ea_AD_142 genes are linked to TIER1_GS 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)
FCS_3ea_AD_142 Exclusive	TIER1_GS	0.91	4.89	8.10	4.98	7.96
TIER1_GS Exclusive	FCS_3ea_AD_142	0.70	4.73	5.49	4.08	7.76
FCS_3ea_AD_142 Exclusive	TIER1_GS Exclusive	0.88	4.24	7.62	5.29	7.30
TIER1_GS Exclusive	FCS_3ea_AD_142 Exclusive	0.68	4.41	4.70	3.87	6.90
FCS_3ea_AD_142 Exclusive	Overlap	1.00	3.94	4.55	3.99	4.47
TIER1_GS Exclusive	Overlap	1.00	2.96	4.29	3.70	4.05
Overlap	Exclusives	0.74	5.40	9.00	4.19	10.63

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)
FCS_3ea_AD_142 Exclusive	TIER1_GS	0.05	49.76	56.32	60.65	121.82
TIER1_GS Exclusive	FCS_3ea_AD_142	0.05	42.17	40.79	43.40	59.66
FCS_3ea_AD_142 Exclusive	TIER1_GS Exclusive	0.02	17.00	38.69	20.46	19.81
TIER1_GS Exclusive	FCS_3ea_AD_142 Exclusive	0.03	26.79	29.14	26.48	30.09
FCS_3ea_AD_142 Exclusive	Overlap	0.07	116.68	73.94	134.97	220.87
TIER1_GS Exclusive	Overlap	0.14	270.75	304.37	601.81	200.65
Overlap	Exclusives	0.10	62.82	120.15	60.24	137.48

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	 
FCS_3ea_AD_142 Exclusive	136	136	
TIER1_GS Exclusive	25	24	MS4A
Overlap	6	6