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)
BRCA-Familial Exclusive	VEPRare2MethodConsensusAC1	1.83e-03	2.22e-01	3.54e-08	1.25e-03
VEPRare2MethodConsensusAC1 Exclusive	BRCA-Familial	7.55e-11	3.34e-10	2.72e-15	8.09e-18
BRCA-Familial Exclusive	VEPRare2MethodConsensusAC1 Exclusive	1.25e-03	6.68e-01	5.69e-09	5.47e-03
VEPRare2MethodConsensusAC1 Exclusive	BRCA-Familial Exclusive	9.13e-08	5.27e-07	7.77e-11	7.53e-13
BRCA-Familial Exclusive	Overlap	2.62e-06	2.62e-06	2.62e-06	3.00e-06
VEPRare2MethodConsensusAC1 Exclusive	Overlap	2.69e-05	1.52e-04	9.81e-06	5.58e-06
Overlap	Exclusives	3.37e-05	8.54e-04	8.14e-16	1.02e-05



Evaluating how well BRCA-Familial genes are linked to VEPRare2MethodConsensusAC1 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)
BRCA-Familial Exclusive	VEPRare2MethodConsensusAC1	0.61	1.20	1.34	1.61	3.79
VEPRare2MethodConsensusAC1 Exclusive	BRCA-Familial	0.98	3.04	6.29	2.52	8.01
BRCA-Familial Exclusive	VEPRare2MethodConsensusAC1 Exclusive	0.59	0.87	1.02	0.98	3.64
VEPRare2MethodConsensusAC1 Exclusive	BRCA-Familial Exclusive	0.97	2.63	6.03	2.63	6.87
BRCA-Familial Exclusive	Overlap	1.00	1.89	4.13	2.76	4.25
VEPRare2MethodConsensusAC1 Exclusive	Overlap	0.99	2.19	3.68	1.78	4.80
Overlap	Exclusives	0.65	2.91	2.89	2.11	5.95

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)
BRCA-Familial Exclusive	VEPRare2MethodConsensusAC1	0.03	15.31	12.54	24.02	28.56
VEPRare2MethodConsensusAC1 Exclusive	BRCA-Familial	0.03	6.26	34.54	13.63	7.66
BRCA-Familial Exclusive	VEPRare2MethodConsensusAC1 Exclusive	0.01	9.94	4.64	9.47	7.49
VEPRare2MethodConsensusAC1 Exclusive	BRCA-Familial Exclusive	0.02	1.88	19.28	8.31	68.83
BRCA-Familial Exclusive	Overlap	0.08	32.68	229.41	146.84	96.56
VEPRare2MethodConsensusAC1 Exclusive	Overlap	0.02	2.39	47.29	7.19	37.59
Overlap	Exclusives	0.04	31.83	37.96	33.48	49.64

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	 
BRCA-Familial Exclusive	17	17	
VEPRare2MethodConsensusAC1 Exclusive	120	119	PRAMEF11
Overlap	6	6