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 Exclusive	GWAS	1.32e-01	1.62e-01	4.78e-02	1.16e-02
GWAS Exclusive	AD	2.10e-01	3.19e-01	3.23e-02	5.71e-02
AD Exclusive	GWAS Exclusive	4.85e-01	4.69e-01	1.21e-01	4.22e-02
GWAS Exclusive	AD Exclusive	9.46e-01	6.51e-01	1.22e-01	1.49e-01
AD Exclusive	Overlap	2.67e-02	3.05e-02	1.62e-02	2.49e-03
GWAS Exclusive	Overlap	1.38e-11	2.39e-10	8.35e-13	8.95e-11
Overlap	Exclusives	5.12e-05	1.94e-06	1.45e-18	7.80e-10



Evaluating how well AD 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 Exclusive	GWAS	0.60	1.14	1.17	0.88	3.23
GWAS Exclusive	AD	0.57	1.56	1.61	1.59	2.50
AD Exclusive	GWAS Exclusive	0.58	0.69	0.70	0.80	2.81
GWAS Exclusive	AD Exclusive	0.54	0.66	0.66	0.58	1.57
AD Exclusive	Overlap	0.83	2.03	1.74	1.84	3.02
GWAS Exclusive	Overlap	1.00	3.65	4.38	3.76	3.99
Overlap	Exclusives	0.65	4.86	6.47	4.04	7.18

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 Exclusive	GWAS	0.01	0.66	1.65	0.88	2.64
GWAS Exclusive	AD	0.02	23.36	23.27	19.05	8.24
AD Exclusive	GWAS Exclusive	0.01	0.41	0.54	0.70	1.76
GWAS Exclusive	AD Exclusive	0.01	0.86	0.89	0.55	0.46
AD Exclusive	Overlap	0.00	3.67	2.34	2.17	1.84
GWAS Exclusive	Overlap	0.17	451.59	420.33	527.84	499.53
Overlap	Exclusives	0.06	59.70	88.03	55.22	80.77

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 Exclusive	95	95	
GWAS Exclusive	103	98	D21S2088E;LINC00158;SLC8A1-AS1;MIR302F;PCDH11Y
Overlap	6	6