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-Somatic	5.73e-08	1.75e-05	7.84e-21	9.94e-23
BRCA-Somatic Exclusive	BRCA-TCGA	2.12e-07	5.10e-07	5.27e-26	2.14e-20
BRCA-TCGA Exclusive	BRCA-Somatic Exclusive	3.79e-06	2.05e-04	7.84e-19	4.57e-19
BRCA-Somatic Exclusive	BRCA-TCGA Exclusive	8.28e-06	1.34e-07	1.09e-23	5.57e-18
BRCA-TCGA Exclusive	Overlap	2.10e-05	2.10e-05	2.10e-05	3.02e-05
BRCA-Somatic Exclusive	Overlap	2.10e-05	2.10e-05	2.10e-05	2.52e-05
Overlap	Exclusives	2.48e-33	2.56e-28	8.05e-52	2.23e-44



Evaluating how well BRCA-TCGA genes are linked to BRCA-Somatic 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-Somatic	0.93	1.23	4.54	3.14	9.50
BRCA-Somatic Exclusive	BRCA-TCGA	0.87	1.83	6.04	2.96	10.71
BRCA-TCGA Exclusive	BRCA-Somatic Exclusive	0.92	1.31	3.69	3.41	9.56
BRCA-Somatic Exclusive	BRCA-TCGA Exclusive	0.86	2.09	6.06	3.34	9.18
BRCA-TCGA Exclusive	Overlap	0.99	1.44	6.88	2.36	3.29
BRCA-Somatic Exclusive	Overlap	0.99	1.83	2.74	2.56	3.56
Overlap	Exclusives	0.94	15.30	11.66	3.34	14.26

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-Somatic	0.03	-0.47	12.30	11.08	37.86
BRCA-Somatic Exclusive	BRCA-TCGA	0.03	0.16	10.32	9.65	30.46
BRCA-TCGA Exclusive	BRCA-Somatic Exclusive	0.02	-0.47	7.95	9.38	49.26
BRCA-Somatic Exclusive	BRCA-TCGA Exclusive	0.02	0.47	7.48	9.58	16.37
BRCA-TCGA Exclusive	Overlap	0.03	-0.08	167.94	28.65	48.06
BRCA-Somatic Exclusive	Overlap	0.02	-0.19	47.45	40.96	8.59
Overlap	Exclusives	0.11	40.24	99.48	35.07	229.88

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	53	53	
BRCA-Somatic Exclusive	35	35	
Overlap	5	5