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)
122AD Exclusive	109GWAS	2.24e-02	3.08e-03	7.38e-05	5.85e-08
109GWAS Exclusive	122AD	1.37e-01	1.35e-01	4.07e-03	4.59e-03
122AD Exclusive	109GWAS Exclusive	5.26e-02	9.51e-03	2.56e-04	9.42e-07
109GWAS Exclusive	122AD Exclusive	4.97e-01	1.79e-01	6.86e-03	8.26e-03
122AD Exclusive	Overlap	2.02e-02	8.15e-02	6.88e-03	1.78e-03
109GWAS Exclusive	Overlap	1.83e-09	1.83e-09	1.83e-09	1.83e-09
Overlap	Exclusives	3.89e-05	2.01e-06	3.06e-28	3.27e-08



Evaluating how well 122AD genes are linked to 109GWAS 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)
122AD Exclusive	109GWAS	0.67	3.03	4.58	3.44	6.09
109GWAS Exclusive	122AD	0.60	2.90	2.30	2.87	3.95
122AD Exclusive	109GWAS Exclusive	0.66	2.71	3.87	3.42	5.44
109GWAS Exclusive	122AD Exclusive	0.58	2.24	1.76	2.61	3.14
122AD Exclusive	Overlap	0.96	2.36	2.59	2.92	3.32
109GWAS Exclusive	Overlap	1.00	3.89	3.42	2.93	3.45
Overlap	Exclusives	0.63	3.19	5.66	2.63	7.36

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)
122AD Exclusive	109GWAS	0.02	5.76	15.85	13.56	15.50
109GWAS Exclusive	122AD	0.03	14.99	22.70	33.36	36.72
122AD Exclusive	109GWAS Exclusive	0.01	6.98	10.99	9.57	5.89
109GWAS Exclusive	122AD Exclusive	0.02	12.72	12.28	10.58	18.64
122AD Exclusive	Overlap	0.01	9.05	4.96	12.74	1.83
109GWAS Exclusive	Overlap	0.15	424.97	235.63	182.69	303.83
Overlap	Exclusives	0.07	45.11	64.03	38.81	86.08

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	 
122AD Exclusive	118	117	RFPL2
109GWAS Exclusive	105	100	PCDH11Y;D21S2088E;LINC00158;SLC8A1-AS1;MIR302F
Overlap	4	4