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)
AD_proxy Exclusive	GWAS	4.92e-04	9.51e-03	4.49e-06	1.38e-05
GWAS Exclusive	AD_proxy	2.97e-01	3.09e-02	1.40e-03	2.08e-04
AD_proxy Exclusive	GWAS Exclusive	1.08e-03	2.78e-02	2.34e-05	2.09e-04
GWAS Exclusive	AD_proxy Exclusive	7.03e-01	6.52e-02	3.67e-03	1.24e-03
AD_proxy Exclusive	Overlap	8.14e-03	1.33e-02	3.61e-03	5.06e-04
GWAS Exclusive	Overlap	7.45e-12	7.45e-12	7.45e-12	7.45e-12
Overlap	Exclusives	2.20e-05	2.20e-05	6.37e-13	1.05e-07



Evaluating how well AD_proxy genes are linked to GWAS 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)
AD_proxy Exclusive	GWAS	0.66	3.28	3.34	2.80	6.02
GWAS Exclusive	AD_proxy	0.62	2.53	3.01	2.96	4.66
AD_proxy Exclusive	GWAS Exclusive	0.64	3.18	2.88	2.49	4.91
GWAS Exclusive	AD_proxy Exclusive	0.60	1.38	2.42	2.18	3.11
AD_proxy Exclusive	Overlap	0.91	3.13	3.37	2.36	3.29
GWAS Exclusive	Overlap	1.00	4.54	4.66	3.51	3.93
Overlap	Exclusives	0.64	3.81	5.53	2.77	7.84

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)
AD_proxy Exclusive	GWAS	0.01	9.45	11.03	8.09	16.18
GWAS Exclusive	AD_proxy	0.04	59.13	60.48	30.73	69.56
AD_proxy Exclusive	GWAS Exclusive	0.01	10.90	8.85	4.67	9.51
GWAS Exclusive	AD_proxy Exclusive	0.02	8.83	23.95	23.78	22.45
AD_proxy Exclusive	Overlap	0.00	7.40	15.81	4.81	1.75
GWAS Exclusive	Overlap	0.25	1199.89	667.74	597.73	597.72
Overlap	Exclusives	0.07	77.70	92.89	44.64	93.72

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	 
AD_proxy Exclusive	90	87	KDM5D;TMEM265;SERPINA3
GWAS Exclusive	104	99	PCDH11Y;D21S2088E;MIR302F;SLC8A1-AS1;LINC00158
Overlap	5	5