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-q0-01 Exclusive	GWAS	2.96e-01	9.46e-01	2.35e-02	1.63e-04
GWAS Exclusive	AllVar2MethodGenes-q0-01	4.27e-01	6.04e-01	2.10e-03	1.09e-03
AllVar2MethodGenes-q0-01 Exclusive	GWAS Exclusive	3.06e-01	9.94e-01	5.20e-02	6.19e-04
GWAS Exclusive	AllVar2MethodGenes-q0-01 Exclusive	3.60e-01	5.41e-01	1.95e-03	2.31e-03
AllVar2MethodGenes-q0-01 Exclusive	Overlap	1.02e-02	1.02e-02	1.02e-02	1.10e-02
GWAS Exclusive	Overlap	1.26e-02	3.26e-02	1.02e-02	1.18e-02
Overlap	Exclusives	9.95e-04	1.61e-04	1.52e-40	1.31e-15



Evaluating how well AllVar2MethodGenes-q0-01 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-q0-01 Exclusive	GWAS	0.61	-0.20	0.17	0.42	4.58
GWAS Exclusive	AllVar2MethodGenes-q0-01	0.62	0.03	0.50	0.47	3.64
AllVar2MethodGenes-q0-01 Exclusive	GWAS Exclusive	0.60	-0.21	0.03	0.42	3.69
GWAS Exclusive	AllVar2MethodGenes-q0-01 Exclusive	0.61	-0.13	0.44	0.44	3.13
AllVar2MethodGenes-q0-01 Exclusive	Overlap	0.80	0.11	0.67	0.47	1.83
GWAS Exclusive	Overlap	0.83	-0.87	-0.41	0.31	2.36
Overlap	Exclusives	0.68	3.24	4.81	3.04	8.81

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-q0-01 Exclusive	GWAS	0.01	-0.10	1.66	1.73	3.54
GWAS Exclusive	AllVar2MethodGenes-q0-01	0.01	1.02	3.59	1.44	6.62
AllVar2MethodGenes-q0-01 Exclusive	GWAS Exclusive	0.01	-0.83	-0.15	0.42	3.81
GWAS Exclusive	AllVar2MethodGenes-q0-01 Exclusive	0.01	-0.06	1.08	1.19	1.11
AllVar2MethodGenes-q0-01 Exclusive	Overlap	0.02	11.15	68.30	40.93	48.46
GWAS Exclusive	Overlap	0.01	3.91	1.72	16.84	8.81
Overlap	Exclusives	0.03	7.20	15.97	9.65	23.74

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-q0-01 Exclusive	72	72	
GWAS Exclusive	164	164	
Overlap	5	4