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)
BRCA-TCGA Exclusive	Rare2MethodConsensus	1.02e-02	8.83e-02	3.37e-06	9.96e-06
Rare2MethodConsensus Exclusive	BRCA-TCGA	1.76e-11	2.95e-10	1.38e-15	1.37e-18
BRCA-TCGA Exclusive	Rare2MethodConsensus Exclusive	9.02e-02	6.96e-02	1.90e-05	1.52e-04
Rare2MethodConsensus Exclusive	BRCA-TCGA Exclusive	2.10e-08	5.88e-08	7.30e-12	2.89e-14
BRCA-TCGA Exclusive	Overlap	4.18e-08	4.18e-08	4.18e-08	5.21e-08
Rare2MethodConsensus Exclusive	Overlap	6.33e-06	7.91e-06	7.74e-07	4.99e-08
Overlap	Exclusives	6.96e-10	7.39e-07	9.39e-29	1.29e-12



Evaluating how well BRCA-TCGA genes are linked to Rare2MethodConsensus 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)
BRCA-TCGA Exclusive	Rare2MethodConsensus	0.64	2.99	3.11	2.98	5.07
Rare2MethodConsensus Exclusive	BRCA-TCGA	0.88	2.75	7.57	3.56	10.71
BRCA-TCGA Exclusive	Rare2MethodConsensus Exclusive	0.62	3.57	2.83	3.22	4.86
Rare2MethodConsensus Exclusive	BRCA-TCGA Exclusive	0.86	2.92	5.71	2.95	8.26
BRCA-TCGA Exclusive	Overlap	1.00	2.01	3.90	2.13	5.29
Rare2MethodConsensus Exclusive	Overlap	1.00	2.09	3.75	2.33	4.61
Overlap	Exclusives	0.68	2.06	6.39	2.89	8.24

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)
BRCA-TCGA Exclusive	Rare2MethodConsensus	0.04	8.27	30.75	29.04	38.01
Rare2MethodConsensus Exclusive	BRCA-TCGA	0.05	8.67	32.41	22.34	24.43
BRCA-TCGA Exclusive	Rare2MethodConsensus Exclusive	0.02	16.36	17.66	13.23	23.09
Rare2MethodConsensus Exclusive	BRCA-TCGA Exclusive	0.02	8.02	29.92	11.05	43.76
BRCA-TCGA Exclusive	Overlap	0.10	1.81	152.60	60.42	50.45
Rare2MethodConsensus Exclusive	Overlap	0.05	4.69	21.63	20.06	16.31
Overlap	Exclusives	0.05	17.15	39.11	19.62	48.33

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	 
BRCA-TCGA Exclusive	50	50	
Rare2MethodConsensus Exclusive	143	140	;C4B_2;SSPO
Overlap	8	8