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	BRCA-TCGA	5.77e-21	5.72e-17	4.75e-34	1.12e-28
BRCA-TCGA Exclusive	BRCA-Familial	1.22e-19	7.24e-14	7.87e-25	2.97e-23
BRCA-Familial Exclusive	BRCA-TCGA Exclusive	2.61e-13	1.31e-10	5.61e-23	4.69e-18
BRCA-TCGA Exclusive	BRCA-Familial Exclusive	1.65e-07	3.51e-05	5.32e-12	2.90e-12
BRCA-Familial Exclusive	Overlap	2.55e-14	6.47e-14	2.44e-14	3.29e-14
BRCA-TCGA Exclusive	Overlap	2.44e-14	8.68e-14	2.44e-14	3.43e-14
Overlap	Exclusives	1.34e-22	8.59e-17	9.72e-33	1.48e-30



Evaluating how well BRCA-Familial genes are linked to BRCA-TCGA 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	BRCA-TCGA	0.93	4.60	8.47	3.89	11.19
BRCA-TCGA Exclusive	BRCA-Familial	0.99	2.74	6.61	3.97	9.93
BRCA-Familial Exclusive	BRCA-TCGA Exclusive	0.91	4.21	5.93	4.65	8.86
BRCA-TCGA Exclusive	BRCA-Familial Exclusive	0.98	2.14	3.83	3.34	7.34
BRCA-Familial Exclusive	Overlap	1.00	2.48	6.18	3.30	6.74
BRCA-TCGA Exclusive	Overlap	1.00	3.08	5.70	2.90	7.27
Overlap	Exclusives	0.92	3.35	9.31	4.82	12.20

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	BRCA-TCGA	0.16	14.19	112.36	74.75	303.86
BRCA-TCGA Exclusive	BRCA-Familial	0.20	7.14	160.76	137.73	532.10
BRCA-Familial Exclusive	BRCA-TCGA Exclusive	0.03	5.68	23.09	28.54	40.48
BRCA-TCGA Exclusive	BRCA-Familial Exclusive	0.03	0.19	20.91	27.90	110.67
BRCA-Familial Exclusive	Overlap	0.37	23.66	443.47	304.00	913.80
BRCA-TCGA Exclusive	Overlap	0.24	34.24	316.60	199.43	547.36
Overlap	Exclusives	0.08	14.54	78.18	63.11	119.30

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	16	16	
BRCA-TCGA Exclusive	43	43	
Overlap	15	15