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-TCGA Exclusive	BRCA-Familial	1.97e-19	6.26e-14	8.84e-25	8.77e-23
BRCA-Familial Exclusive	BRCA-TCGA	1.53e-20	3.85e-17	4.91e-34	5.90e-29
BRCA-TCGA Exclusive	BRCA-Familial Exclusive	2.87e-07	3.51e-05	3.38e-12	4.93e-12
BRCA-Familial Exclusive	BRCA-TCGA Exclusive	1.24e-12	1.13e-10	7.22e-23	6.93e-18
BRCA-TCGA Exclusive	Overlap	2.44e-14	6.47e-14	2.44e-14	2.77e-14
BRCA-Familial Exclusive	Overlap	2.44e-14	6.47e-14	2.44e-14	3.58e-14
Overlap	Exclusives	2.22e-22	2.47e-17	1.57e-32	2.91e-29



Evaluating how well BRCA-TCGA 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-TCGA Exclusive	BRCA-Familial	0.99	2.88	7.39	3.22	9.34
BRCA-Familial Exclusive	BRCA-TCGA	0.93	4.24	9.08	4.07	11.88
BRCA-TCGA Exclusive	BRCA-Familial Exclusive	0.98	2.01	3.97	3.88	7.20
BRCA-Familial Exclusive	BRCA-TCGA Exclusive	0.91	4.08	7.09	4.61	8.72
BRCA-TCGA Exclusive	Overlap	1.00	2.63	6.18	3.00	5.66
BRCA-Familial Exclusive	Overlap	1.00	2.23	6.57	2.99	6.73
Overlap	Exclusives	0.92	3.06	8.94	4.44	11.61

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-TCGA Exclusive	BRCA-Familial	0.20	9.46	165.22	98.53	292.90
BRCA-Familial Exclusive	BRCA-TCGA	0.16	13.74	115.42	97.42	301.53
BRCA-TCGA Exclusive	BRCA-Familial Exclusive	0.03	0.16	22.87	36.51	108.49
BRCA-Familial Exclusive	BRCA-TCGA Exclusive	0.03	4.73	26.17	38.02	54.46
BRCA-TCGA Exclusive	Overlap	0.24	15.32	339.53	189.48	543.39
BRCA-Familial Exclusive	Overlap	0.37	19.54	551.16	249.09	1247.51
Overlap	Exclusives	0.08	12.79	78.09	44.29	40.09

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-TCGA Exclusive	43	43	
BRCA-Familial Exclusive	16	16	
Overlap	15	15