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-gwas	9.77e-05	1.60e-02	1.81e-23	4.95e-12
BRCA-gwas Exclusive	TCGA-MC3-BRCA-AllCoreGenes	2.86e-07	1.55e-06	2.77e-34	1.51e-44
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-gwas Exclusive	4.33e-04	3.44e-02	9.35e-21	8.52e-09
BRCA-gwas Exclusive	TCGA-MC3-BRCA-AllCoreGenes Exclusive	2.00e-06	8.19e-07	1.24e-32	9.37e-42
TCGA-MC3-BRCA-AllCoreGenes Exclusive	Overlap	8.99e-05	1.40e-02	9.59e-24	1.51e-13
BRCA-gwas Exclusive	Overlap	1.99e-03	3.08e-03	1.86e-06	7.89e-08
Overlap	Exclusives	2.31e-24	1.49e-20	5.38e-98	3.08e-69



Evaluating how well TCGA-MC3-BRCA-AllCoreGenes 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)
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-gwas	0.66	1.80	2.91	3.60	8.42
BRCA-gwas Exclusive	TCGA-MC3-BRCA-AllCoreGenes	0.80	1.62	5.75	3.35	18.09
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-gwas Exclusive	0.64	1.69	2.05	3.22	6.03
BRCA-gwas Exclusive	TCGA-MC3-BRCA-AllCoreGenes Exclusive	0.80	1.52	5.46	3.66	15.86
TCGA-MC3-BRCA-AllCoreGenes Exclusive	Overlap	0.98	3.34	3.59	2.97	5.52
BRCA-gwas Exclusive	Overlap	0.93	1.26	2.15	2.12	5.02
Overlap	Exclusives	0.79	5.06	14.24	4.39	20.26

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)
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-gwas	0.03	0.82	10.56	10.93	20.58
BRCA-gwas Exclusive	TCGA-MC3-BRCA-AllCoreGenes	0.09	3.75	25.67	13.36	90.46
TCGA-MC3-BRCA-AllCoreGenes Exclusive	BRCA-gwas Exclusive	0.02	1.99	4.72	7.44	10.17
BRCA-gwas Exclusive	TCGA-MC3-BRCA-AllCoreGenes Exclusive	0.07	2.66	20.19	12.56	62.74
TCGA-MC3-BRCA-AllCoreGenes Exclusive	Overlap	0.06	0.79	43.69	13.81	71.29
BRCA-gwas Exclusive	Overlap	0.10	7.05	23.45	51.45	249.45
Overlap	Exclusives	0.08	7.46	28.74	15.65	72.06

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	206	206	
BRCA-gwas Exclusive	162	162	
Overlap	11	11