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)
Rare2MethodGenes Exclusive	BRCA-Familial	1.26e-08	2.75e-08	3.37e-13	7.96e-19
BRCA-Familial Exclusive	Rare2MethodGenes	1.15e-03	8.37e-02	1.73e-08	6.42e-04
Rare2MethodGenes Exclusive	BRCA-Familial Exclusive	2.63e-05	3.81e-05	8.44e-09	1.30e-12
BRCA-Familial Exclusive	Rare2MethodGenes Exclusive	4.78e-03	5.62e-01	2.23e-08	8.82e-03
Rare2MethodGenes Exclusive	Overlap	6.74e-05	3.58e-04	7.48e-06	3.97e-08
BRCA-Familial Exclusive	Overlap	5.81e-09	3.36e-07	5.33e-09	1.51e-08
Overlap	Exclusives	2.10e-05	1.05e-03	3.68e-20	1.76e-07



Evaluating how well Rare2MethodGenes genes are linked to BRCA-Familial 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)
Rare2MethodGenes Exclusive	BRCA-Familial	0.96	2.14	5.61	2.73	9.50
BRCA-Familial Exclusive	Rare2MethodGenes	0.61	2.38	1.38	1.61	4.50
Rare2MethodGenes Exclusive	BRCA-Familial Exclusive	0.95	2.09	5.32	2.98	7.37
BRCA-Familial Exclusive	Rare2MethodGenes Exclusive	0.59	2.62	0.92	1.19	3.87
Rare2MethodGenes Exclusive	Overlap	0.99	2.06	3.67	2.31	4.34
BRCA-Familial Exclusive	Overlap	1.00	2.19	4.22	3.05	5.08
Overlap	Exclusives	0.65	1.64	3.49	2.43	6.08

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)
Rare2MethodGenes Exclusive	BRCA-Familial	0.05	2.25	35.18	9.09	102.86
BRCA-Familial Exclusive	Rare2MethodGenes	0.05	30.75	59.96	46.86	68.32
Rare2MethodGenes Exclusive	BRCA-Familial Exclusive	0.02	1.57	23.46	10.18	28.56
BRCA-Familial Exclusive	Rare2MethodGenes Exclusive	0.02	26.03	17.38	14.72	19.18
Rare2MethodGenes Exclusive	Overlap	0.04	2.70	34.74	11.62	64.65
BRCA-Familial Exclusive	Overlap	0.26	34.43	420.66	315.09	844.03
Overlap	Exclusives	0.03	12.09	26.94	22.31	18.50

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	 
Rare2MethodGenes Exclusive	142	139	;SSPO;C4B_2
BRCA-Familial Exclusive	22	22	
Overlap	9	9