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 Exclusive	tier1_31	4.08e-13	3.36e-12	1.18e-13	1.36e-13
tier1_31 Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered	3.10e-02	5.79e-02	1.44e-02	4.34e-03
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered Exclusive	tier1_31 Exclusive	2.54e-10	1.22e-10	8.32e-11	3.36e-10
tier1_31 Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered Exclusive	1.65e-01	7.29e-02	3.59e-02	2.02e-02
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered Exclusive	Overlap	1.28e-07	6.40e-08	6.40e-08	1.28e-07
tier1_31 Exclusive	Overlap	1.83e-09	1.83e-09	1.83e-09	9.14e-09
Overlap	Exclusives	1.17e-07	5.94e-07	4.50e-22	1.38e-08



Evaluating how well Sigma_EA_AD_APOE34_HC_APOE3_agefiltered genes are linked to tier1_31 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 Exclusive	tier1_31	0.88	5.47	7.59	4.86	7.17
tier1_31 Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered	0.58	2.95	2.37	2.29	2.65
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered Exclusive	tier1_31 Exclusive	0.86	4.60	6.68	4.31	6.74
tier1_31 Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered Exclusive	0.56	2.29	1.90	1.88	2.29
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered Exclusive	Overlap	1.00	2.51	3.50	2.71	3.19
tier1_31 Exclusive	Overlap	1.00	2.92	3.68	3.45	3.53
Overlap	Exclusives	0.66	6.06	7.27	3.96	6.28

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 Exclusive	tier1_31	0.03	47.79	43.29	46.52	7.19
tier1_31 Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered	0.04	41.99	46.08	18.63	45.85
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered Exclusive	tier1_31 Exclusive	0.02	29.01	51.04	26.06	14.30
tier1_31 Exclusive	Sigma_EA_AD_APOE34_HC_APOE3_agefiltered Exclusive	0.03	42.70	32.43	35.18	29.38
Sigma_EA_AD_APOE34_HC_APOE3_agefiltered Exclusive	Overlap	0.03	37.79	39.88	34.91	60.30
tier1_31 Exclusive	Overlap	0.10	218.32	175.14	52.13	75.36
Overlap	Exclusives	0.10	110.40	168.27	74.19	160.39

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 Exclusive	111	108	IQCJ-SCHIP1;RFPL2;AC099811.2
tier1_31 Exclusive	27	26	MS4A
Overlap	4	4