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)
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-somatic	3.89e-12	6.06e-11	2.74e-42	9.69e-33
BRCA-somatic Exclusive	TCGA-MC3-BRCA-AllCoreGenes	5.32e-31	7.13e-21	7.28e-95	1.08e-67
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-somatic Exclusive	4.87e-09	3.90e-07	3.12e-27	1.29e-23
BRCA-somatic Exclusive	TCGA-MC3-BRCA-AllCoreGenes Exclusive	2.35e-28	1.72e-19	1.16e-87	4.49e-63
TCGA-MC3-BRCA-AllCoreGenes Exclusive	Overlap	3.08e-07	2.53e-05	6.87e-24	4.27e-12
BRCA-somatic Exclusive	Overlap	6.13e-10	7.00e-09	2.42e-18	3.22e-10
Overlap	Exclusives	7.81e-56	1.17e-33	2.79e-127	3.86e-106



Evaluating how well TCGA-MC3-BRCA-AllCoreGenes 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)
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-somatic	0.97	2.44	6.16	4.36	9.76
BRCA-somatic Exclusive	TCGA-MC3-BRCA-AllCoreGenes	0.87	3.41	12.17	5.70	18.96
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-somatic Exclusive	0.96	1.70	4.82	3.62	7.75
BRCA-somatic Exclusive	TCGA-MC3-BRCA-AllCoreGenes Exclusive	0.86	3.13	12.19	5.08	17.16
TCGA-MC3-BRCA-AllCoreGenes Exclusive	Overlap	0.98	3.20	3.93	3.77	5.19
BRCA-somatic Exclusive	Overlap	0.99	2.50	4.56	3.89	5.09
Overlap	Exclusives	0.91	8.69	18.85	5.21	20.85

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)
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-somatic	0.15	2.68	45.29	32.08	381.93
BRCA-somatic Exclusive	TCGA-MC3-BRCA-AllCoreGenes	0.10	5.26	25.25	26.19	116.29
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-somatic Exclusive	0.06	-0.74	21.49	11.22	166.61
BRCA-somatic Exclusive	TCGA-MC3-BRCA-AllCoreGenes Exclusive	0.08	4.55	25.03	23.00	71.58
TCGA-MC3-BRCA-AllCoreGenes Exclusive	Overlap	0.19	18.51	398.12	89.07	139.33
BRCA-somatic Exclusive	Overlap	0.04	2.46	95.70	87.25	120.38
Overlap	Exclusives	0.15	22.79	66.99	37.40	180.06

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	 
TCGA-MC3-BRCA-AllCoreGenes Exclusive	207	207	
BRCA-somatic Exclusive	27	27	
Overlap	10	10