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-q0-01 Exclusive	BRCA-All-GS	4.49e-05	9.40e-05	2.79e-08	9.32e-17
BRCA-All-GS Exclusive	Common2MethodGenes-q0-01	3.99e-04	2.56e-03	1.25e-05	1.12e-03
Common2MethodGenes-q0-01 Exclusive	BRCA-All-GS Exclusive	4.94e-04	1.23e-03	2.09e-06	7.74e-15
BRCA-All-GS Exclusive	Common2MethodGenes-q0-01 Exclusive	7.73e-02	2.42e-01	5.52e-04	1.25e-02
Common2MethodGenes-q0-01 Exclusive	Overlap	2.64e-06	4.02e-06	2.64e-06	4.02e-06
BRCA-All-GS Exclusive	Overlap	2.64e-06	1.28e-05	2.64e-06	3.45e-06
Overlap	Exclusives	5.20e-11	9.44e-12	6.07e-37	3.28e-33



Evaluating how well Common2MethodGenes-q0-01 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-q0-01 Exclusive	BRCA-All-GS	0.68	1.23	4.29	1.83	9.33
BRCA-All-GS Exclusive	Common2MethodGenes-q0-01	0.68	1.85	1.88	1.45	4.67
Common2MethodGenes-q0-01 Exclusive	BRCA-All-GS Exclusive	0.67	1.44	4.09	1.80	9.50
BRCA-All-GS Exclusive	Common2MethodGenes-q0-01 Exclusive	0.64	1.73	1.52	1.15	3.25
Common2MethodGenes-q0-01 Exclusive	Overlap	0.91	2.06	3.89	2.00	4.20
BRCA-All-GS Exclusive	Overlap	0.92	1.27	1.99	2.05	3.60
Overlap	Exclusives	0.74	3.28	9.06	3.57	12.96

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-q0-01 Exclusive	BRCA-All-GS	0.03	3.10	16.04	5.76	14.47
BRCA-All-GS Exclusive	Common2MethodGenes-q0-01	0.10	83.41	128.64	119.36	182.71
Common2MethodGenes-q0-01 Exclusive	BRCA-All-GS Exclusive	0.03	2.73	12.85	4.21	15.48
BRCA-All-GS Exclusive	Common2MethodGenes-q0-01 Exclusive	0.01	22.14	16.73	15.88	22.00
Common2MethodGenes-q0-01 Exclusive	Overlap	0.02	16.32	52.19	32.15	11.28
BRCA-All-GS Exclusive	Overlap	0.42	132.59	138.62	377.70	320.39
Overlap	Exclusives	0.07	9.56	38.91	16.08	51.22

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-q0-01 Exclusive	44	44	
BRCA-All-GS Exclusive	249	249	
Overlap	9	8