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)
Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	TIER1_GS	6.05e-01	4.83e-01	4.86e-01	4.71e-02
TIER1_GS Exclusive	Sigma_EA_APOE3_excluding_WCAP_99	1.57e-01	3.69e-01	2.19e-01	1.03e-01
Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	TIER1_GS Exclusive	4.36e-01	3.59e-01	4.47e-01	4.04e-02
TIER1_GS Exclusive	Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	1.54e-01	4.55e-01	1.84e-01	1.06e-01
Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	Overlap	7.72e-01	3.76e-01	1.78e-01	3.17e-01
TIER1_GS Exclusive	Overlap	1.98e-02	1.98e-02	1.98e-02	1.98e-02
Overlap	Exclusives	4.62e-05	1.84e-04	5.55e-06	2.60e-05



Evaluating how well Sigma_EA_APOE3_excluding_WCAP_99 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)
Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	TIER1_GS	0.60	0.03	-0.07	0.31	1.94
TIER1_GS Exclusive	Sigma_EA_APOE3_excluding_WCAP_99	0.55	0.31	0.64	0.54	1.60
Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	TIER1_GS Exclusive	0.60	-0.09	-0.33	0.10	1.89
TIER1_GS Exclusive	Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	0.54	0.26	0.33	0.49	1.41
Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	Overlap	0.85	0.65	1.23	1.40	1.13
TIER1_GS Exclusive	Overlap	1.00	1.75	1.85	2.18	1.93
Overlap	Exclusives	0.62	2.44	3.42	2.52	4.54

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)
Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	TIER1_GS	0.00	0.39	0.27	1.29	1.31
TIER1_GS Exclusive	Sigma_EA_APOE3_excluding_WCAP_99	0.01	1.06	1.70	1.50	2.06
Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	TIER1_GS Exclusive	0.00	0.55	-0.03	0.43	2.05
TIER1_GS Exclusive	Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	0.01	-0.14	0.14	0.26	0.67
Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	Overlap	0.00	-0.12	0.00	-0.02	0.16
TIER1_GS Exclusive	Overlap	0.06	17.29	99.66	266.18	37.74
Overlap	Exclusives	0.03	13.61	33.91	12.37	20.20

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	 
Sigma_EA_APOE3_excluding_WCAP_99 Exclusive	98	97	RFPL2
TIER1_GS Exclusive	30	29	MS4A
Overlap	1	1