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-GWAS Exclusive	BRCA-Familial	1.42e-02	7.55e-02	2.28e-07	4.16e-11
BRCA-Familial Exclusive	BRCA-GWAS	8.49e-03	4.14e-04	1.43e-15	6.44e-14
BRCA-GWAS Exclusive	BRCA-Familial Exclusive	1.22e-01	1.34e-01	1.32e-05	1.63e-09
BRCA-Familial Exclusive	BRCA-GWAS Exclusive	2.97e-02	2.11e-04	3.21e-15	8.82e-13
BRCA-GWAS Exclusive	Overlap	3.70e-03	6.56e-03	1.38e-03	1.45e-03
BRCA-Familial Exclusive	Overlap	1.38e-03	1.38e-03	1.38e-03	1.53e-03
Overlap	Exclusives	7.02e-05	1.85e-05	3.39e-41	4.17e-19



Evaluating how well BRCA-GWAS 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)
BRCA-GWAS Exclusive	BRCA-Familial	0.93	1.28	3.20	2.08	8.08
BRCA-Familial Exclusive	BRCA-GWAS	0.69	3.33	5.12	3.50	7.68
BRCA-GWAS Exclusive	BRCA-Familial Exclusive	0.92	1.29	3.25	1.70	6.21
BRCA-Familial Exclusive	BRCA-GWAS Exclusive	0.68	3.29	4.37	4.58	8.34
BRCA-GWAS Exclusive	Overlap	0.99	1.21	2.66	1.40	2.75
BRCA-Familial Exclusive	Overlap	1.00	1.43	2.85	2.39	3.11
Overlap	Exclusives	0.72	2.95	6.66	2.67	10.86

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-GWAS Exclusive	BRCA-Familial	0.13	5.95	10.38	41.45	106.79
BRCA-Familial Exclusive	BRCA-GWAS	0.02	1.28	5.76	7.71	16.02
BRCA-GWAS Exclusive	BRCA-Familial Exclusive	0.13	4.66	14.29	46.24	94.58
BRCA-Familial Exclusive	BRCA-GWAS Exclusive	0.02	1.00	5.06	6.98	12.96
BRCA-GWAS Exclusive	Overlap	0.02	2.37	0.33	14.37	56.47
BRCA-Familial Exclusive	Overlap	0.03	6.07	65.56	40.21	24.43
Overlap	Exclusives	0.03	5.86	19.75	9.98	21.89

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-GWAS Exclusive	170	169	
BRCA-Familial Exclusive	20	20	
Overlap	3	3