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)
AllVar2MethodGenes Exclusive	GWAS	9.53e-02	7.92e-01	3.86e-02	2.04e-04
GWAS Exclusive	AllVar2MethodGenes	1.80e-01	8.96e-01	5.28e-04	6.80e-02
AllVar2MethodGenes Exclusive	GWAS Exclusive	1.14e-01	7.52e-01	5.90e-02	4.74e-04
GWAS Exclusive	AllVar2MethodGenes Exclusive	3.15e-01	9.75e-01	1.54e-03	7.99e-02
AllVar2MethodGenes Exclusive	Overlap	3.22e-02	3.22e-02	3.22e-02	3.50e-02
GWAS Exclusive	Overlap	4.11e-02	8.58e-02	3.22e-02	3.05e-02
Overlap	Exclusives	7.48e-04	4.82e-04	2.57e-32	1.41e-12



Evaluating how well AllVar2MethodGenes 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)
AllVar2MethodGenes Exclusive	GWAS	0.61	-0.49	0.21	0.40	5.61
GWAS Exclusive	AllVar2MethodGenes	0.56	-0.62	0.09	0.62	1.99
AllVar2MethodGenes Exclusive	GWAS Exclusive	0.61	-0.28	-0.05	0.42	4.59
GWAS Exclusive	AllVar2MethodGenes Exclusive	0.55	-0.77	0.04	0.13	2.21
AllVar2MethodGenes Exclusive	Overlap	0.78	0.15	0.58	0.45	2.31
GWAS Exclusive	Overlap	0.82	-0.34	0.38	1.05	2.47
Overlap	Exclusives	0.64	3.24	5.09	2.66	9.02

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)
AllVar2MethodGenes Exclusive	GWAS	0.01	-0.30	1.66	0.83	7.80
GWAS Exclusive	AllVar2MethodGenes	0.01	0.55	2.39	2.09	3.76
AllVar2MethodGenes Exclusive	GWAS Exclusive	0.01	-1.15	-0.36	0.02	4.80
GWAS Exclusive	AllVar2MethodGenes Exclusive	0.01	-0.14	0.87	0.85	1.40
AllVar2MethodGenes Exclusive	Overlap	0.02	31.04	72.24	32.77	31.05
GWAS Exclusive	Overlap	0.01	1.37	2.04	15.14	44.72
Overlap	Exclusives	0.03	7.41	14.45	8.07	12.47

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	 
AllVar2MethodGenes Exclusive	131	129	DKK 3.00;GPR75-ASB3
GWAS Exclusive	163	163	
Overlap	6	5