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)
AllVar2MethodGenes-q0-01 Exclusive	BRCA-All-GS	8.26e-05	6.89e-04	3.73e-07	1.57e-13
BRCA-All-GS Exclusive	AllVar2MethodGenes-q0-01	1.62e-04	1.11e-03	6.06e-07	5.01e-04
AllVar2MethodGenes-q0-01 Exclusive	BRCA-All-GS Exclusive	3.61e-03	1.47e-02	7.67e-05	5.14e-13
BRCA-All-GS Exclusive	AllVar2MethodGenes-q0-01 Exclusive	1.11e-02	1.36e-01	4.86e-04	9.32e-03
AllVar2MethodGenes-q0-01 Exclusive	Overlap	3.36e-07	3.92e-07	3.36e-07	3.63e-07
BRCA-All-GS Exclusive	Overlap	3.36e-07	1.59e-06	3.36e-07	3.92e-07
Overlap	Exclusives	6.52e-13	1.55e-13	1.41e-29	7.37e-32



Evaluating how well AllVar2MethodGenes-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)
AllVar2MethodGenes-q0-01 Exclusive	BRCA-All-GS	0.67	1.05	2.82	1.36	10.36
BRCA-All-GS Exclusive	AllVar2MethodGenes-q0-01	0.66	1.35	2.15	1.44	4.63
AllVar2MethodGenes-q0-01 Exclusive	BRCA-All-GS Exclusive	0.66	0.94	2.49	1.17	9.43
BRCA-All-GS Exclusive	AllVar2MethodGenes-q0-01 Exclusive	0.62	1.52	1.37	0.96	3.21
AllVar2MethodGenes-q0-01 Exclusive	Overlap	0.91	1.91	3.45	1.72	4.19
BRCA-All-GS Exclusive	Overlap	0.93	1.29	2.36	2.20	4.47
Overlap	Exclusives	0.73	4.24	8.99	3.88	15.40

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)
AllVar2MethodGenes-q0-01 Exclusive	BRCA-All-GS	0.04	5.02	20.34	7.48	30.42
BRCA-All-GS Exclusive	AllVar2MethodGenes-q0-01	0.08	56.79	111.46	76.42	147.47
AllVar2MethodGenes-q0-01 Exclusive	BRCA-All-GS Exclusive	0.03	2.28	13.23	3.32	20.39
BRCA-All-GS Exclusive	AllVar2MethodGenes-q0-01 Exclusive	0.01	15.80	14.76	9.11	13.64
AllVar2MethodGenes-q0-01 Exclusive	Overlap	0.05	56.59	62.87	55.96	214.62
BRCA-All-GS Exclusive	Overlap	0.41	71.26	158.63	333.29	455.33
Overlap	Exclusives	0.07	11.83	39.92	20.23	45.06

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	 
AllVar2MethodGenes-q0-01 Exclusive	67	67	
BRCA-All-GS Exclusive	248	248	
Overlap	10	9