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-Familial	6.71e-11	3.06e-10	1.48e-15	1.49e-17
BRCA-Familial Exclusive	vep_2method_RareCon_AC1	1.73e-03	2.23e-01	6.00e-09	1.23e-03
vep_2method_RareCon_AC1 Exclusive	BRCA-Familial Exclusive	1.87e-07	5.73e-07	4.77e-11	4.78e-13
BRCA-Familial Exclusive	vep_2method_RareCon_AC1 Exclusive	1.19e-03	7.36e-01	2.42e-09	5.03e-03
vep_2method_RareCon_AC1 Exclusive	Overlap	2.10e-05	1.00e-04	4.10e-06	4.68e-06
BRCA-Familial Exclusive	Overlap	2.62e-06	2.62e-06	2.62e-06	2.74e-06
Overlap	Exclusives	2.71e-05	6.76e-04	4.39e-17	2.08e-05



Evaluating how well vep_2method_RareCon_AC1 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)
vep_2method_RareCon_AC1 Exclusive	BRCA-Familial	0.98	2.74	6.44	2.89	8.40
BRCA-Familial Exclusive	vep_2method_RareCon_AC1	0.61	1.13	1.29	1.36	4.27
vep_2method_RareCon_AC1 Exclusive	BRCA-Familial Exclusive	0.97	2.44	5.60	2.75	6.90
BRCA-Familial Exclusive	vep_2method_RareCon_AC1 Exclusive	0.59	0.80	0.96	1.11	3.66
vep_2method_RareCon_AC1 Exclusive	Overlap	0.99	2.14	3.53	2.22	4.32
BRCA-Familial Exclusive	Overlap	1.00	2.01	3.94	2.63	3.88
Overlap	Exclusives	0.65	3.08	2.82	1.94	5.97

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-Familial	0.03	5.18	33.76	15.70	72.77
BRCA-Familial Exclusive	vep_2method_RareCon_AC1	0.03	21.70	14.01	16.66	29.46
vep_2method_RareCon_AC1 Exclusive	BRCA-Familial Exclusive	0.02	2.84	20.40	12.71	19.81
BRCA-Familial Exclusive	vep_2method_RareCon_AC1 Exclusive	0.01	9.14	5.94	9.81	13.20
vep_2method_RareCon_AC1 Exclusive	Overlap	0.02	11.41	37.65	18.11	28.37
BRCA-Familial Exclusive	Overlap	0.08	24.29	199.65	95.21	120.55
Overlap	Exclusives	0.04	32.87	39.71	25.88	48.21

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-Familial Exclusive	17	17	
Overlap	6	6