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)
vep_2method_RareCon_AC1 Exclusive	BRCA-GWAS	5.67e-02	1.20e-01	9.54e-06	7.47e-07
BRCA-GWAS Exclusive	vep_2method_RareCon_AC1	4.88e-01	6.12e-01	3.91e-04	1.64e-04
vep_2method_RareCon_AC1 Exclusive	BRCA-GWAS Exclusive	4.26e-02	1.46e-01	5.03e-05	1.47e-05
BRCA-GWAS Exclusive	vep_2method_RareCon_AC1 Exclusive	4.89e-01	7.26e-01	2.98e-04	4.02e-03
vep_2method_RareCon_AC1 Exclusive	Overlap	6.77e-02	7.74e-02	2.24e-03	4.26e-04
BRCA-GWAS Exclusive	Overlap	7.91e-02	2.97e-01	4.86e-03	1.05e-03
Overlap	Exclusives	8.12e-02	2.04e-03	1.58e-53	2.58e-11



Evaluating how well vep_2method_RareCon_AC1 genes are linked to BRCA-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)
vep_2method_RareCon_AC1 Exclusive	BRCA-GWAS	0.61	-0.16	0.17	0.94	4.75
BRCA-GWAS Exclusive	vep_2method_RareCon_AC1	0.60	0.22	0.63	0.85	3.71
vep_2method_RareCon_AC1 Exclusive	BRCA-GWAS Exclusive	0.60	-0.33	-0.11	0.59	4.32
BRCA-GWAS Exclusive	vep_2method_RareCon_AC1 Exclusive	0.58	0.02	0.47	0.74	2.89
vep_2method_RareCon_AC1 Exclusive	Overlap	0.94	1.70	2.40	1.89	3.87
BRCA-GWAS Exclusive	Overlap	0.93	0.70	1.33	1.52	3.72
Overlap	Exclusives	0.64	1.89	4.03	2.57	8.48

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)
vep_2method_RareCon_AC1 Exclusive	BRCA-GWAS	0.02	0.73	2.40	3.64	5.48
BRCA-GWAS Exclusive	vep_2method_RareCon_AC1	0.01	1.16	2.05	3.21	6.42
vep_2method_RareCon_AC1 Exclusive	BRCA-GWAS Exclusive	0.01	0.34	1.14	2.15	6.19
BRCA-GWAS Exclusive	vep_2method_RareCon_AC1 Exclusive	0.01	0.61	1.08	1.97	1.67
vep_2method_RareCon_AC1 Exclusive	Overlap	0.01	6.70	10.67	10.28	56.80
BRCA-GWAS Exclusive	Overlap	0.01	1.40	0.08	9.43	13.09
Overlap	Exclusives	0.03	3.74	11.77	8.43	17.16

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	 
vep_2method_RareCon_AC1 Exclusive	120	119	PRAMEF11
BRCA-GWAS Exclusive	167	167	
Overlap	6	6