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)
Common2MethodGenes Exclusive	BRCA-All-GS	1.85e-06	5.62e-05	9.61e-08	1.18e-13
BRCA-All-GS Exclusive	Common2MethodGenes	9.23e-05	8.61e-04	1.73e-07	3.74e-04
Common2MethodGenes Exclusive	BRCA-All-GS Exclusive	9.93e-05	1.51e-03	1.22e-05	9.34e-13
BRCA-All-GS Exclusive	Common2MethodGenes Exclusive	8.08e-03	8.16e-02	6.47e-05	7.23e-02
Common2MethodGenes Exclusive	Overlap	3.36e-07	5.99e-07	3.36e-07	4.95e-07
BRCA-All-GS Exclusive	Overlap	3.36e-07	1.54e-06	3.36e-07	5.34e-07
Overlap	Exclusives	1.40e-10	1.72e-12	1.71e-27	3.12e-30



Evaluating how well Common2MethodGenes 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)
Common2MethodGenes Exclusive	BRCA-All-GS	0.67	1.33	3.77	1.95	11.03
BRCA-All-GS Exclusive	Common2MethodGenes	0.63	1.60	1.91	1.65	4.96
Common2MethodGenes Exclusive	BRCA-All-GS Exclusive	0.66	1.25	2.87	1.93	9.22
BRCA-All-GS Exclusive	Common2MethodGenes Exclusive	0.59	1.47	1.36	0.83	2.95
Common2MethodGenes Exclusive	Overlap	0.93	2.48	3.82	2.56	4.15
BRCA-All-GS Exclusive	Overlap	0.94	2.41	3.12	2.86	4.57
Overlap	Exclusives	0.71	3.05	8.44	3.49	14.58

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)
Common2MethodGenes Exclusive	BRCA-All-GS	0.04	5.96	22.17	7.81	32.29
BRCA-All-GS Exclusive	Common2MethodGenes	0.06	66.33	85.27	40.45	123.46
Common2MethodGenes Exclusive	BRCA-All-GS Exclusive	0.03	3.40	14.67	5.86	24.56
BRCA-All-GS Exclusive	Common2MethodGenes Exclusive	0.01	19.24	17.24	5.02	14.35
Common2MethodGenes Exclusive	Overlap	0.05	55.32	45.88	67.58	65.12
BRCA-All-GS Exclusive	Overlap	0.37	123.24	105.80	414.07	688.24
Overlap	Exclusives	0.08	9.33	43.55	18.10	62.88

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	 
Common2MethodGenes Exclusive	79	79	
BRCA-All-GS Exclusive	253	253	
Overlap	9	9