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-TCGA	8.63e-06	1.58e-03	2.71e-14	3.56e-15
BRCA-TCGA Exclusive	BRCA-GWAS	4.08e-03	8.29e-03	9.66e-14	1.48e-10
BRCA-GWAS Exclusive	BRCA-TCGA Exclusive	2.52e-04	1.17e-03	3.91e-12	3.39e-13
BRCA-TCGA Exclusive	BRCA-GWAS Exclusive	2.05e-02	1.10e-02	2.78e-12	1.11e-08
BRCA-GWAS Exclusive	Overlap	2.57e-03	3.14e-02	4.31e-05	6.41e-05
BRCA-TCGA Exclusive	Overlap	1.35e-03	1.31e-02	4.93e-05	1.50e-04
Overlap	Exclusives	7.68e-10	8.98e-11	1.91e-43	1.11e-24



Evaluating how well BRCA-GWAS 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-GWAS Exclusive	BRCA-TCGA	0.85	1.84	5.09	2.40	8.52
BRCA-TCGA Exclusive	BRCA-GWAS	0.67	2.16	2.81	3.48	7.72
BRCA-GWAS Exclusive	BRCA-TCGA Exclusive	0.84	1.68	4.21	3.52	7.94
BRCA-TCGA Exclusive	BRCA-GWAS Exclusive	0.66	2.12	2.94	3.14	8.08
BRCA-GWAS Exclusive	Overlap	0.98	2.00	1.70	2.32	4.61
BRCA-TCGA Exclusive	Overlap	0.97	1.94	2.38	2.33	3.71
Overlap	Exclusives	0.74	2.38	10.19	3.14	13.26

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-GWAS Exclusive	BRCA-TCGA	0.06	4.55	11.61	20.29	106.33
BRCA-TCGA Exclusive	BRCA-GWAS	0.02	0.23	4.47	9.17	17.61
BRCA-GWAS Exclusive	BRCA-TCGA Exclusive	0.05	3.87	36.97	29.22	111.78
BRCA-TCGA Exclusive	BRCA-GWAS Exclusive	0.02	-0.21	4.52	5.87	9.79
BRCA-GWAS Exclusive	Overlap	0.01	3.27	0.48	10.09	65.07
BRCA-TCGA Exclusive	Overlap	0.02	7.39	38.58	59.52	52.05
Overlap	Exclusives	0.05	5.16	35.04	16.94	44.26

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	164	163	
BRCA-TCGA Exclusive	53	53	
Overlap	5	5