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)
APOE3_analysis_positive Exclusive	tier1_31	7.50e-04	9.52e-06	1.18e-05	4.03e-07
tier1_31 Exclusive	APOE3_analysis_positive	2.97e-01	2.21e-01	3.70e-02	3.61e-02
APOE3_analysis_positive Exclusive	tier1_31 Exclusive	1.64e-03	4.30e-05	1.02e-05	2.81e-06
tier1_31 Exclusive	APOE3_analysis_positive Exclusive	4.63e-01	2.84e-01	6.24e-02	8.05e-02
APOE3_analysis_positive Exclusive	Overlap	3.17e-01	9.90e-02	3.96e-02	1.19e-01
tier1_31 Exclusive	Overlap	1.98e-02	1.98e-02	1.98e-02	1.98e-02
Overlap	Exclusives	2.04e-11	5.81e-10	1.60e-11	2.55e-12



Evaluating how well APOE3_analysis_positive 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)
APOE3_analysis_positive Exclusive	tier1_31	0.76	2.10	4.21	2.29	4.41
tier1_31 Exclusive	APOE3_analysis_positive	0.61	2.24	2.12	2.04	3.08
APOE3_analysis_positive Exclusive	tier1_31 Exclusive	0.75	1.76	4.36	2.30	4.84
tier1_31 Exclusive	APOE3_analysis_positive Exclusive	0.61	2.33	1.89	2.22	2.59
APOE3_analysis_positive Exclusive	Overlap	0.95	1.25	2.22	2.02	1.60
tier1_31 Exclusive	Overlap	1.00	1.86	1.70	2.09	1.79
Overlap	Exclusives	0.74	2.73	6.67	3.10	6.31

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)
APOE3_analysis_positive Exclusive	tier1_31	0.00	1.57	3.14	2.48	0.28
tier1_31 Exclusive	APOE3_analysis_positive	0.01	7.39	4.71	6.12	6.46
APOE3_analysis_positive Exclusive	tier1_31 Exclusive	0.00	0.55	3.81	1.25	2.02
tier1_31 Exclusive	APOE3_analysis_positive Exclusive	0.00	4.36	3.20	4.29	2.87
APOE3_analysis_positive Exclusive	Overlap	0.00	-0.03	1.23	4.83	2.05
tier1_31 Exclusive	Overlap	0.06	191.83	43.88	441.81	52.54
Overlap	Exclusives	0.04	14.83	43.57	19.95	60.60

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	 
APOE3_analysis_positive Exclusive	48	48	
tier1_31 Exclusive	30	29	MS4A
Overlap	1	1