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_agefiltered_excluding_WCAP_88 Exclusive	TIER1_GS	3.01e-01	1.80e-01	3.84e-01	1.26e-02
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88	3.08e-01	4.06e-01	2.04e-01	2.44e-01
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88 Exclusive	TIER1_GS Exclusive	5.30e-01	1.43e-01	4.43e-01	1.05e-02
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88 Exclusive	6.55e-01	6.14e-01	6.23e-01	5.62e-01
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88 Exclusive	Overlap	7.89e-01	7.13e-01	8.01e-01	2.89e-01
TIER1_GS Exclusive	Overlap	4.36e-07	4.36e-07	4.36e-07	1.74e-06
Overlap	Exclusives	1.18e-05	1.04e-05	1.17e-13	1.34e-05



Evaluating how well Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88 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_agefiltered_excluding_WCAP_88 Exclusive	TIER1_GS	0.65	1.52	1.87	0.90	2.93
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88	0.55	1.73	1.53	1.34	1.76
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88 Exclusive	TIER1_GS Exclusive	0.64	1.12	2.19	0.90	2.81
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88 Exclusive	0.54	1.20	1.09	1.07	1.02
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88 Exclusive	Overlap	0.79	1.18	1.19	0.78	1.69
TIER1_GS Exclusive	Overlap	1.00	2.90	2.46	3.19	2.81
Overlap	Exclusives	0.63	3.58	4.57	3.15	5.85

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_agefiltered_excluding_WCAP_88 Exclusive	TIER1_GS	0.00	1.40	1.28	0.57	1.57
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88	0.01	7.66	10.30	7.93	10.25
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88 Exclusive	TIER1_GS Exclusive	0.00	0.69	0.93	0.13	0.82
TIER1_GS Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88 Exclusive	0.00	0.90	1.26	1.01	1.00
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered_excluding_WCAP_88 Exclusive	Overlap	0.00	3.70	5.05	3.22	8.49
TIER1_GS Exclusive	Overlap	0.10	212.13	137.38	303.11	155.24
Overlap	Exclusives	0.07	79.20	110.13	82.22	136.17

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_agefiltered_excluding_WCAP_88 Exclusive	85	81	RFPL2;AC099811.2;AC093155.3;IQCJ-SCHIP1
TIER1_GS Exclusive	28	27	MS4A
Overlap	3	3