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_WESr2_median_10random_z35 Exclusive	tier1_31	9.31e-01	9.93e-01	6.66e-01	1.76e-01
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z35	4.16e-01	9.53e-02	8.19e-02	7.65e-02
APOE3_AD_WESr2_median_10random_z35 Exclusive	tier1_31 Exclusive	7.77e-01	9.23e-01	9.25e-01	6.33e-02
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z35 Exclusive	5.71e-01	1.08e-01	7.02e-02	1.33e-01
APOE3_AD_WESr2_median_10random_z35 Exclusive	Overlap	4.16e-01	6.34e-01	7.52e-01	9.50e-01
tier1_31 Exclusive	Overlap	1.98e-02	1.98e-02	1.98e-02	1.98e-02
Overlap	Exclusives	3.28e-09	2.91e-08	7.08e-10	1.01e-09



Evaluating how well APOE3_AD_WESr2_median_10random_z35 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_WESr2_median_10random_z35 Exclusive	tier1_31	0.62	0.36	0.45	0.77	2.35
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z35	0.56	0.34	1.13	1.17	1.48
APOE3_AD_WESr2_median_10random_z35 Exclusive	tier1_31 Exclusive	0.63	0.65	0.70	0.26	2.24
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z35 Exclusive	0.55	0.25	1.02	1.21	1.17
APOE3_AD_WESr2_median_10random_z35 Exclusive	Overlap	0.46	-0.82	-0.70	-0.46	-0.02
tier1_31 Exclusive	Overlap	1.00	1.71	1.79	2.14	1.66
Overlap	Exclusives	0.71	2.63	5.26	2.80	6.20

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_WESr2_median_10random_z35 Exclusive	tier1_31	0.00	-0.03	-0.32	0.40	0.36
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z35	0.00	2.49	3.51	0.61	2.37
APOE3_AD_WESr2_median_10random_z35 Exclusive	tier1_31 Exclusive	0.00	0.17	-0.06	-0.14	1.18
tier1_31 Exclusive	APOE3_AD_WESr2_median_10random_z35 Exclusive	0.00	-0.07	0.36	0.44	0.51
APOE3_AD_WESr2_median_10random_z35 Exclusive	Overlap	0.00	-0.53	-0.27	-0.26	-0.20
tier1_31 Exclusive	Overlap	0.06	65.16	73.73	201.85	138.51
Overlap	Exclusives	0.04	8.79	58.53	26.61	54.68

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_WESr2_median_10random_z35 Exclusive	45	43	AC093155.3;RFPL2
tier1_31 Exclusive	30	29	MS4A
Overlap	1	1