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_APOE44_HC_APOE33_balanced Exclusive	tier1_31	5.59e-01	6.60e-01	5.65e-01	3.87e-02
tier1_31 Exclusive	Sigma_EA_AD_APOE44_HC_APOE33_balanced	7.03e-02	2.61e-01	6.21e-01	5.72e-01
Sigma_EA_AD_APOE44_HC_APOE33_balanced Exclusive	tier1_31 Exclusive	6.08e-01	6.51e-01	4.28e-01	3.75e-02
tier1_31 Exclusive	Sigma_EA_AD_APOE44_HC_APOE33_balanced Exclusive	7.01e-02	3.43e-01	6.00e-01	4.73e-01
Sigma_EA_AD_APOE44_HC_APOE33_balanced Exclusive	Overlap	1.78e-01	1.98e-02	1.19e-01	5.94e-02
tier1_31 Exclusive	Overlap	1.98e-02	1.98e-02	1.98e-02	1.98e-02
Overlap	Exclusives	2.17e-04	1.28e-07	1.04e-26	3.82e-08



Evaluating how well Sigma_EA_AD_APOE44_HC_APOE33_balanced 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_APOE44_HC_APOE33_balanced Exclusive	tier1_31	0.59	-0.28	-0.34	-0.13	1.41
tier1_31 Exclusive	Sigma_EA_AD_APOE44_HC_APOE33_balanced	0.49	-0.38	-0.71	-0.46	-0.39
Sigma_EA_AD_APOE44_HC_APOE33_balanced Exclusive	tier1_31 Exclusive	0.57	-0.22	-0.33	-0.22	1.28
tier1_31 Exclusive	Sigma_EA_AD_APOE44_HC_APOE33_balanced Exclusive	0.48	-0.35	-0.69	-0.49	-0.35
Sigma_EA_AD_APOE44_HC_APOE33_balanced Exclusive	Overlap	0.98	1.06	inf	1.18	1.75
tier1_31 Exclusive	Overlap	1.00	1.37	inf	1.61	1.98
Overlap	Exclusives	0.64	432770860652826.00	5.05	2.73	4.85

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_APOE44_HC_APOE33_balanced Exclusive	tier1_31	0.00	-0.48	-0.41	-0.36	0.03
tier1_31 Exclusive	Sigma_EA_AD_APOE44_HC_APOE33_balanced	0.00	-0.01	0.06	-0.03	0.22
Sigma_EA_AD_APOE44_HC_APOE33_balanced Exclusive	tier1_31 Exclusive	0.00	-0.50	-0.43	-0.46	-0.14
tier1_31 Exclusive	Sigma_EA_AD_APOE44_HC_APOE33_balanced Exclusive	0.00	-0.27	-0.59	-0.30	-0.32
Sigma_EA_AD_APOE44_HC_APOE33_balanced Exclusive	Overlap	0.00	1.21	3548223919023563.00	0.96	3.20
tier1_31 Exclusive	Overlap	0.02	37.15	151272923003761312.00	79.98	30.10
Overlap	Exclusives	0.02	4400120241935670.50	6.25	6.42	17.88

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_APOE44_HC_APOE33_balanced Exclusive	60	60	
tier1_31 Exclusive	30	29	MS4A
Overlap	1	1