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)
Rare2MethodGenes Exclusive	BRCA-All-GS	7.81e-05	6.84e-04	3.06e-09	1.81e-18
BRCA-All-GS Exclusive	Rare2MethodGenes	5.44e-03	1.26e-01	1.24e-09	2.21e-05
Rare2MethodGenes Exclusive	BRCA-All-GS Exclusive	1.60e-03	8.26e-03	5.87e-08	1.04e-16
BRCA-All-GS Exclusive	Rare2MethodGenes Exclusive	3.96e-02	4.99e-01	4.23e-07	6.54e-03
Rare2MethodGenes Exclusive	Overlap	3.04e-04	1.84e-03	2.37e-05	2.93e-07
BRCA-All-GS Exclusive	Overlap	4.92e-08	1.33e-06	1.43e-09	2.56e-10
Overlap	Exclusives	2.04e-13	5.17e-11	2.00e-41	1.64e-29



Evaluating how well Rare2MethodGenes 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)
Rare2MethodGenes Exclusive	BRCA-All-GS	0.70	1.94	4.53	2.45	10.69
BRCA-All-GS Exclusive	Rare2MethodGenes	0.63	2.63	2.89	2.92	6.15
Rare2MethodGenes Exclusive	BRCA-All-GS Exclusive	0.68	1.37	3.15	2.38	10.46
BRCA-All-GS Exclusive	Rare2MethodGenes Exclusive	0.59	1.74	1.81	2.48	3.70
Rare2MethodGenes Exclusive	Overlap	0.91	1.72	2.88	2.47	5.54
BRCA-All-GS Exclusive	Overlap	0.98	3.52	3.86	3.15	6.76
Overlap	Exclusives	0.69	3.64	7.33	3.91	15.80

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)
Rare2MethodGenes Exclusive	BRCA-All-GS	0.04	2.53	14.04	5.76	29.16
BRCA-All-GS Exclusive	Rare2MethodGenes	0.06	14.85	63.65	49.00	93.65
Rare2MethodGenes Exclusive	BRCA-All-GS Exclusive	0.03	1.59	9.48	4.00	21.79
BRCA-All-GS Exclusive	Rare2MethodGenes Exclusive	0.01	6.47	5.72	6.91	6.80
Rare2MethodGenes Exclusive	Overlap	0.02	3.73	11.86	12.29	9.86
BRCA-All-GS Exclusive	Overlap	0.40	12.18	192.72	119.99	999.01
Overlap	Exclusives	0.07	8.55	26.05	19.11	46.74

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	 
Rare2MethodGenes Exclusive	136	134	C4B_2;SSPO
BRCA-All-GS Exclusive	243	243	
Overlap	15	14