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	7.09e-05	5.91e-04	1.91e-06	1.43e-13
BRCA-All-GS Exclusive	Common2MethodGenes	3.23e-04	2.10e-03	4.86e-07	7.72e-04
Common2MethodGenes Exclusive	BRCA-All-GS Exclusive	4.25e-03	1.11e-02	1.01e-04	5.53e-12
BRCA-All-GS Exclusive	Common2MethodGenes Exclusive	2.06e-02	1.53e-01	8.21e-05	6.33e-02
Common2MethodGenes Exclusive	Overlap	3.36e-07	5.55e-07	3.36e-07	5.34e-07
BRCA-All-GS Exclusive	Overlap	3.36e-07	2.30e-06	3.36e-07	4.41e-07
Overlap	Exclusives	1.57e-10	1.55e-11	2.17e-27	2.62e-31



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	1.28	3.13	1.53	9.98
BRCA-All-GS Exclusive	Common2MethodGenes	0.63	1.82	1.84	1.20	4.50
Common2MethodGenes Exclusive	BRCA-All-GS Exclusive	0.66	0.71	2.53	1.10	7.81
BRCA-All-GS Exclusive	Common2MethodGenes Exclusive	0.59	1.76	1.00	0.82	2.72
Common2MethodGenes Exclusive	Overlap	0.93	2.47	3.95	2.37	4.48
BRCA-All-GS Exclusive	Overlap	0.92	1.92	2.71	2.32	4.13
Overlap	Exclusives	0.72	3.27	7.02	3.53	13.95

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	4.12	17.25	7.13	24.27
BRCA-All-GS Exclusive	Common2MethodGenes	0.06	55.17	95.42	69.34	121.67
Common2MethodGenes Exclusive	BRCA-All-GS Exclusive	0.03	2.04	11.68	4.01	16.70
BRCA-All-GS Exclusive	Common2MethodGenes Exclusive	0.01	17.65	13.07	9.76	9.28
Common2MethodGenes Exclusive	Overlap	0.03	44.52	37.53	42.14	65.48
BRCA-All-GS Exclusive	Overlap	0.37	139.50	104.87	358.99	874.76
Overlap	Exclusives	0.07	8.94	37.02	21.30	67.72

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	73	73	
BRCA-All-GS Exclusive	248	248	
Overlap	10	9