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)
AllVar2MethodGenes Exclusive	BRCA-All-GS	2.17e-04	4.48e-03	5.17e-07	7.10e-17
BRCA-All-GS Exclusive	AllVar2MethodGenes	8.19e-04	6.70e-03	1.05e-08	3.71e-03
AllVar2MethodGenes Exclusive	BRCA-All-GS Exclusive	3.04e-03	4.25e-02	2.80e-05	2.19e-15
BRCA-All-GS Exclusive	AllVar2MethodGenes Exclusive	1.31e-02	2.37e-01	5.99e-06	5.63e-02
AllVar2MethodGenes Exclusive	Overlap	2.32e-07	3.31e-07	2.32e-07	3.19e-07
BRCA-All-GS Exclusive	Overlap	2.32e-07	1.07e-06	1.02e-07	3.31e-07
Overlap	Exclusives	4.52e-13	1.20e-11	7.69e-30	1.43e-27



Evaluating how well AllVar2MethodGenes genes are linked to BRCA-All-GS 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)
AllVar2MethodGenes Exclusive	BRCA-All-GS	0.68	1.32	2.87	1.54	10.07
BRCA-All-GS Exclusive	AllVar2MethodGenes	0.59	1.01	1.25	1.27	3.21
AllVar2MethodGenes Exclusive	BRCA-All-GS Exclusive	0.67	1.16	2.38	1.46	8.44
BRCA-All-GS Exclusive	AllVar2MethodGenes Exclusive	0.56	0.41	0.85	0.67	2.28
AllVar2MethodGenes Exclusive	Overlap	0.89	2.03	3.59	1.87	4.19
BRCA-All-GS Exclusive	Overlap	0.93	1.38	2.78	2.25	4.73
Overlap	Exclusives	0.70	4.06	9.01	4.25	13.30

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)
AllVar2MethodGenes Exclusive	BRCA-All-GS	0.04	3.74	13.94	4.77	32.39
BRCA-All-GS Exclusive	AllVar2MethodGenes	0.06	48.87	76.26	46.91	76.31
AllVar2MethodGenes Exclusive	BRCA-All-GS Exclusive	0.03	1.73	8.59	2.63	18.17
BRCA-All-GS Exclusive	AllVar2MethodGenes Exclusive	0.01	10.22	8.24	3.74	8.03
AllVar2MethodGenes Exclusive	Overlap	0.04	32.67	49.36	50.86	49.63
BRCA-All-GS Exclusive	Overlap	0.42	87.22	176.88	375.75	579.93
Overlap	Exclusives	0.07	11.21	41.06	21.98	43.63

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	 
AllVar2MethodGenes Exclusive	125	123	GPR75-ASB3;DKK 3.00
BRCA-All-GS Exclusive	246	246	
Overlap	12	11