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-GWAS	4.98e-03	1.56e-02	1.92e-13	9.75e-11
BRCA-GWAS Exclusive	BRCA-TCGA	3.81e-05	7.70e-04	5.05e-15	5.63e-15
BRCA-TCGA Exclusive	BRCA-GWAS Exclusive	1.39e-02	9.57e-03	4.27e-12	2.26e-08
BRCA-GWAS Exclusive	BRCA-TCGA Exclusive	2.06e-04	1.00e-03	7.06e-12	4.02e-13
BRCA-TCGA Exclusive	Overlap	1.35e-03	1.16e-02	5.62e-05	1.17e-04
BRCA-GWAS Exclusive	Overlap	2.57e-03	1.67e-02	4.13e-05	6.99e-05
Overlap	Exclusives	1.92e-09	1.29e-10	4.74e-41	1.78e-24



Evaluating how well BRCA-TCGA genes are linked to BRCA-GWAS 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-GWAS	0.67	2.66	2.91	3.15	7.36
BRCA-GWAS Exclusive	BRCA-TCGA	0.85	1.75	4.63	2.77	10.31
BRCA-TCGA Exclusive	BRCA-GWAS Exclusive	0.66	2.14	2.84	2.82	7.52
BRCA-GWAS Exclusive	BRCA-TCGA Exclusive	0.84	1.75	5.40	3.26	8.38
BRCA-TCGA Exclusive	Overlap	0.97	1.93	2.30	2.34	4.05
BRCA-GWAS Exclusive	Overlap	0.98	2.13	1.96	2.28	3.79
Overlap	Exclusives	0.74	2.67	10.15	2.91	13.01

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-GWAS	0.02	0.20	4.25	7.95	12.98
BRCA-GWAS Exclusive	BRCA-TCGA	0.06	4.65	12.39	22.76	79.56
BRCA-TCGA Exclusive	BRCA-GWAS Exclusive	0.02	-0.18	3.35	5.53	11.78
BRCA-GWAS Exclusive	BRCA-TCGA Exclusive	0.05	3.66	33.24	24.68	73.53
BRCA-TCGA Exclusive	Overlap	0.02	5.78	36.78	43.89	56.14
BRCA-GWAS Exclusive	Overlap	0.01	3.07	0.63	9.34	17.02
Overlap	Exclusives	0.05	6.09	32.78	15.02	52.58

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-GWAS Exclusive	164	163	
Overlap	5	5