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)
EAML_AD_72 Exclusive	TIER1_GS	5.83e-14	5.72e-13	1.18e-13	3.00e-13
TIER1_GS Exclusive	EAML_AD_72	2.82e-01	3.67e-01	2.44e-01	3.15e-01
EAML_AD_72 Exclusive	TIER1_GS Exclusive	3.38e-12	2.25e-12	5.06e-12	1.31e-11
TIER1_GS Exclusive	EAML_AD_72 Exclusive	6.09e-01	6.72e-01	3.25e-01	4.83e-01
EAML_AD_72 Exclusive	Overlap	9.85e-05	5.91e-04	9.85e-05	9.85e-05
TIER1_GS Exclusive	Overlap	9.85e-05	9.85e-05	9.85e-05	2.96e-04
Overlap	Exclusives	4.44e-08	2.11e-08	6.72e-19	2.96e-10



Evaluating how well EAML_AD_72 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)
EAML_AD_72 Exclusive	TIER1_GS	0.88	4.81	7.39	4.85	7.95
TIER1_GS Exclusive	EAML_AD_72	0.53	2.15	1.01	1.05	0.94
EAML_AD_72 Exclusive	TIER1_GS Exclusive	0.87	4.35	7.76	3.97	6.97
TIER1_GS Exclusive	EAML_AD_72 Exclusive	0.52	1.63	0.72	1.13	0.49
EAML_AD_72 Exclusive	Overlap	0.99	2.67	2.41	2.12	2.64
TIER1_GS Exclusive	Overlap	1.00	2.41	1.93	2.54	2.85
Overlap	Exclusives	0.67	5.50	6.93	2.84	5.98

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)
EAML_AD_72 Exclusive	TIER1_GS	0.02	39.02	71.86	33.02	26.22
TIER1_GS Exclusive	EAML_AD_72	0.04	84.25	76.34	39.83	73.73
EAML_AD_72 Exclusive	TIER1_GS Exclusive	0.02	23.54	47.82	17.51	4.37
TIER1_GS Exclusive	EAML_AD_72 Exclusive	0.03	60.84	74.83	44.58	42.38
EAML_AD_72 Exclusive	Overlap	0.01	26.42	5.06	17.38	29.73
TIER1_GS Exclusive	Overlap	0.05	136.67	234.71	277.07	47.89
Overlap	Exclusives	0.06	22.89	107.22	40.78	35.70

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	 
EAML_AD_72 Exclusive	70	68	RFPL2;AL162417.1
TIER1_GS Exclusive	29	28	MS4A
Overlap	2	2