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	1.81e-05	2.86e-04	5.72e-07	5.54e-13
BRCA-All-GS Exclusive	Common2MethodGenes	2.22e-04	1.87e-03	7.95e-07	9.17e-04
Common2MethodGenes Exclusive	BRCA-All-GS Exclusive	5.81e-04	7.17e-03	4.54e-05	3.71e-11
BRCA-All-GS Exclusive	Common2MethodGenes Exclusive	1.38e-02	1.42e-01	1.16e-04	7.87e-02
Common2MethodGenes Exclusive	Overlap	3.36e-07	5.55e-07	3.36e-07	4.41e-07
BRCA-All-GS Exclusive	Overlap	3.36e-07	1.65e-06	3.36e-07	4.24e-07
Overlap	Exclusives	1.65e-10	5.27e-12	3.72e-27	3.50e-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	1.47	3.25	1.39	8.85
BRCA-All-GS Exclusive	Common2MethodGenes	0.62	1.92	2.26	1.37	3.86
Common2MethodGenes Exclusive	BRCA-All-GS Exclusive	0.66	1.00	2.49	1.35	9.66
BRCA-All-GS Exclusive	Common2MethodGenes Exclusive	0.59	1.18	1.25	0.81	2.84
Common2MethodGenes Exclusive	Overlap	0.93	2.38	3.76	2.53	4.36
BRCA-All-GS Exclusive	Overlap	0.94	2.44	2.87	2.40	4.75
Overlap	Exclusives	0.71	3.21	9.34	3.46	14.37

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	6.49	23.51	7.09	26.81
BRCA-All-GS Exclusive	Common2MethodGenes	0.06	71.13	87.72	63.65	103.69
Common2MethodGenes Exclusive	BRCA-All-GS Exclusive	0.03	3.21	12.12	4.94	25.21
BRCA-All-GS Exclusive	Common2MethodGenes Exclusive	0.01	16.75	16.90	9.24	16.79
Common2MethodGenes Exclusive	Overlap	0.04	59.31	44.07	69.15	36.00
BRCA-All-GS Exclusive	Overlap	0.37	112.46	98.84	241.02	1470.74
Overlap	Exclusives	0.07	9.78	45.25	20.86	67.03

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	78	
BRCA-All-GS Exclusive	253	253	
Overlap	9	9