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-TCGA	2.13e-11	2.34e-10	7.46e-15	5.83e-19
BRCA-TCGA Exclusive	Rare2MethodGenes	1.05e-02	8.02e-02	4.84e-06	7.17e-06
Rare2MethodGenes Exclusive	BRCA-TCGA Exclusive	2.29e-08	4.12e-08	1.04e-11	4.17e-14
BRCA-TCGA Exclusive	Rare2MethodGenes Exclusive	1.21e-01	7.28e-02	2.33e-04	4.29e-05
Rare2MethodGenes Exclusive	Overlap	7.08e-06	9.52e-06	1.25e-06	7.72e-08
BRCA-TCGA Exclusive	Overlap	4.18e-08	4.18e-08	4.18e-08	4.37e-08
Overlap	Exclusives	9.92e-10	1.19e-06	6.62e-29	2.72e-12



Evaluating how well Rare2MethodGenes genes are linked to BRCA-TCGA 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-TCGA	0.88	2.65	6.69	3.01	10.18
BRCA-TCGA Exclusive	Rare2MethodGenes	0.64	3.48	2.93	2.98	5.74
Rare2MethodGenes Exclusive	BRCA-TCGA Exclusive	0.86	2.85	6.39	3.07	9.23
BRCA-TCGA Exclusive	Rare2MethodGenes Exclusive	0.62	3.36	3.13	2.60	5.72
Rare2MethodGenes Exclusive	Overlap	1.00	1.67	3.77	2.28	4.82
BRCA-TCGA Exclusive	Overlap	1.00	1.91	3.25	2.23	5.10
Overlap	Exclusives	0.68	2.40	5.08	3.26	7.87

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-TCGA	0.05	7.76	36.73	17.81	75.79
BRCA-TCGA Exclusive	Rare2MethodGenes	0.04	12.58	25.42	26.03	40.30
Rare2MethodGenes Exclusive	BRCA-TCGA Exclusive	0.02	8.09	26.04	13.50	10.79
BRCA-TCGA Exclusive	Rare2MethodGenes Exclusive	0.02	11.98	17.09	16.35	22.17
Rare2MethodGenes Exclusive	Overlap	0.05	2.01	19.48	19.14	121.97
BRCA-TCGA Exclusive	Overlap	0.10	2.28	154.92	38.84	425.95
Overlap	Exclusives	0.05	20.47	33.71	26.86	31.02

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	143	140	;SSPO;C4B_2
BRCA-TCGA Exclusive	50	50	
Overlap	8	8