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_AD_APOE34_HC_APOE3_118 Exclusive	TIER1_GS	2.81e-10	1.83e-10	2.51e-10	2.96e-11
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_118	4.12e-01	3.62e-01	1.63e-01	1.45e-01
Sigma_EA_AD_APOE34_HC_APOE3_118 Exclusive	TIER1_GS Exclusive	5.91e-09	1.25e-09	1.87e-09	2.04e-09
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_118 Exclusive	4.46e-01	5.32e-01	3.01e-01	2.29e-01
Sigma_EA_AD_APOE34_HC_APOE3_118 Exclusive	Overlap	1.00e-03	7.71e-02	1.59e-04	1.98e-04
TIER1_GS Exclusive	Overlap	4.36e-07	4.36e-07	4.36e-07	4.36e-07
Overlap	Exclusives	8.01e-05	6.07e-06	2.63e-19	1.89e-07



Evaluating how well Sigma_EA_AD_APOE34_HC_APOE3_118 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_AD_APOE34_HC_APOE3_118 Exclusive	TIER1_GS	0.84	4.61	7.12	3.97	5.89
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_118	0.55	1.75	1.42	1.71	1.65
Sigma_EA_AD_APOE34_HC_APOE3_118 Exclusive	TIER1_GS Exclusive	0.83	4.52	6.33	3.96	6.10
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_118 Exclusive	0.54	1.26	1.14	1.19	1.23
Sigma_EA_AD_APOE34_HC_APOE3_118 Exclusive	Overlap	0.99	2.61	2.69	2.79	2.69
TIER1_GS Exclusive	Overlap	1.00	2.84	2.63	2.77	2.90
Overlap	Exclusives	0.64	3.52	6.08	3.45	4.96

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_AD_APOE34_HC_APOE3_118 Exclusive	TIER1_GS	0.02	37.93	69.05	28.47	16.44
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_118	0.03	44.85	46.50	47.24	45.99
Sigma_EA_AD_APOE34_HC_APOE3_118 Exclusive	TIER1_GS Exclusive	0.02	31.26	42.51	25.61	36.65
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_118 Exclusive	0.02	30.16	32.96	25.50	28.38
Sigma_EA_AD_APOE34_HC_APOE3_118 Exclusive	Overlap	0.01	21.68	30.90	28.08	7.36
TIER1_GS Exclusive	Overlap	0.10	312.16	159.09	313.70	379.04
Overlap	Exclusives	0.09	69.28	142.84	74.46	119.43

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_AD_APOE34_HC_APOE3_118 Exclusive	115	114	RFPL2
TIER1_GS Exclusive	28	27	MS4A
Overlap	3	3