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_AD_APOE4_HC_77 Exclusive	tier1_31	2.00e-02	6.42e-03	1.63e-03	1.10e-04
tier1_31 Exclusive	APOE3_AD_APOE4_HC_77	9.19e-02	2.51e-01	9.58e-03	2.87e-02
APOE3_AD_APOE4_HC_77 Exclusive	tier1_31 Exclusive	2.74e-02	5.29e-03	5.90e-03	8.91e-05
tier1_31 Exclusive	APOE3_AD_APOE4_HC_77 Exclusive	2.09e-01	5.16e-01	3.92e-02	1.35e-01
APOE3_AD_APOE4_HC_77 Exclusive	Overlap	6.76e-01	7.67e-01	5.57e-01	2.75e-01
tier1_31 Exclusive	Overlap	4.36e-07	4.36e-07	4.36e-07	4.36e-07
Overlap	Exclusives	1.51e-05	6.49e-06	1.21e-14	1.47e-06



Evaluating how well APOE3_AD_APOE4_HC_77 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_AD_APOE4_HC_77 Exclusive	tier1_31	0.73	2.23	3.17	1.86	4.15
tier1_31 Exclusive	APOE3_AD_APOE4_HC_77	0.57	1.45	1.11	1.34	2.37
APOE3_AD_APOE4_HC_77 Exclusive	tier1_31 Exclusive	0.73	2.00	3.26	1.84	4.24
tier1_31 Exclusive	APOE3_AD_APOE4_HC_77 Exclusive	0.56	0.85	0.40	0.60	1.62
APOE3_AD_APOE4_HC_77 Exclusive	Overlap	0.76	1.02	0.96	0.82	1.68
tier1_31 Exclusive	Overlap	1.00	3.55	2.40	3.12	2.91
Overlap	Exclusives	0.68	4.01	5.44	3.02	6.19

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_AD_APOE4_HC_77 Exclusive	tier1_31	0.01	6.57	11.04	3.63	3.97
tier1_31 Exclusive	APOE3_AD_APOE4_HC_77	0.01	12.46	12.22	11.28	9.52
APOE3_AD_APOE4_HC_77 Exclusive	tier1_31 Exclusive	0.00	3.50	8.74	2.39	5.03
tier1_31 Exclusive	APOE3_AD_APOE4_HC_77 Exclusive	0.01	3.10	3.58	2.22	3.30
APOE3_AD_APOE4_HC_77 Exclusive	Overlap	0.01	21.68	50.36	11.32	1.39
tier1_31 Exclusive	Overlap	0.04	129.53	143.00	192.24	236.11
Overlap	Exclusives	0.04	46.19	45.37	19.32	52.10

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_AD_APOE4_HC_77 Exclusive	74	73	CHURC1-FNTB
tier1_31 Exclusive	28	27	MS4A
Overlap	3	3