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_APOE4_HC_APOE3 Exclusive	TIER1_GS	4.09e-06	2.09e-06	6.20e-06	1.50e-07
TIER1_GS Exclusive	Sigma_EA_AD_APOE4_HC_APOE3	3.45e-01	7.03e-02	3.97e-02	4.04e-02
Sigma_EA_AD_APOE4_HC_APOE3 Exclusive	TIER1_GS Exclusive	1.13e-05	1.28e-06	3.37e-06	1.68e-06
TIER1_GS Exclusive	Sigma_EA_AD_APOE4_HC_APOE3 Exclusive	6.35e-01	1.09e-01	4.31e-02	5.91e-02
Sigma_EA_AD_APOE4_HC_APOE3 Exclusive	Overlap	9.38e-02	8.49e-02	9.07e-02	1.34e-02
TIER1_GS Exclusive	Overlap	4.36e-07	4.36e-07	4.36e-07	4.36e-07
Overlap	Exclusives	4.10e-04	1.11e-04	1.68e-19	2.18e-05



Evaluating how well Sigma_EA_AD_APOE4_HC_APOE3 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_APOE4_HC_APOE3 Exclusive	TIER1_GS	0.79	3.56	5.23	2.58	5.33
TIER1_GS Exclusive	Sigma_EA_AD_APOE4_HC_APOE3	0.56	2.68	2.18	2.07	2.26
Sigma_EA_AD_APOE4_HC_APOE3 Exclusive	TIER1_GS Exclusive	0.77	3.59	4.43	3.02	5.39
TIER1_GS Exclusive	Sigma_EA_AD_APOE4_HC_APOE3 Exclusive	0.55	2.33	1.96	2.23	2.11
Sigma_EA_AD_APOE4_HC_APOE3 Exclusive	Overlap	0.94	1.99	1.85	2.20	2.74
TIER1_GS Exclusive	Overlap	1.00	2.63	2.43	2.86	2.73
Overlap	Exclusives	0.63	2.87	6.35	3.24	5.15

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_APOE4_HC_APOE3 Exclusive	TIER1_GS	0.01	13.60	25.30	8.58	14.14
TIER1_GS Exclusive	Sigma_EA_AD_APOE4_HC_APOE3	0.02	27.81	28.05	25.02	22.11
Sigma_EA_AD_APOE4_HC_APOE3 Exclusive	TIER1_GS Exclusive	0.01	16.63	19.94	11.37	14.24
TIER1_GS Exclusive	Sigma_EA_AD_APOE4_HC_APOE3 Exclusive	0.02	17.79	16.75	17.58	15.89
Sigma_EA_AD_APOE4_HC_APOE3 Exclusive	Overlap	0.00	6.13	7.21	2.56	18.20
TIER1_GS Exclusive	Overlap	0.10	267.82	102.79	245.67	213.80
Overlap	Exclusives	0.08	58.16	107.03	66.61	102.75

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_APOE4_HC_APOE3 Exclusive	114	113	RFPL2
TIER1_GS Exclusive	28	27	MS4A
Overlap	3	3