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)
EAML-Common Exclusive	BRCA-All-GS	5.29e-02	8.55e-02	2.91e-06	5.36e-06
BRCA-All-GS Exclusive	EAML-Common	8.59e-04	1.26e-01	9.84e-04	1.59e-02
EAML-Common Exclusive	BRCA-All-GS Exclusive	1.16e-01	1.20e-01	5.01e-06	5.21e-06
BRCA-All-GS Exclusive	EAML-Common Exclusive	1.11e-03	1.32e-01	4.47e-03	3.87e-03
EAML-Common Exclusive	Overlap	9.26e-01	6.19e-01	3.72e-01	7.14e-01
BRCA-All-GS Exclusive	Overlap	3.01e-02	6.47e-02	5.01e-03	3.58e-02
Overlap	Exclusives	2.58e-04	1.15e-03	4.35e-09	5.02e-12



Evaluating how well EAML-Common 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)
EAML-Common Exclusive	BRCA-All-GS	0.59	-1.55	-3.14	-2.61	4.91
BRCA-All-GS Exclusive	EAML-Common	0.44	-1.51	-2.05	-2.12	-3.64
EAML-Common Exclusive	BRCA-All-GS Exclusive	0.59	-1.67	-3.00	-2.59	5.72
BRCA-All-GS Exclusive	EAML-Common Exclusive	0.43	-1.85	-2.39	-2.37	-4.05
EAML-Common Exclusive	Overlap	0.53	0.30	-0.52	-0.38	0.25
BRCA-All-GS Exclusive	Overlap	0.73	0.61	1.56	2.02	2.19
Overlap	Exclusives	0.59	1.59	3.39	1.67	6.80

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)
EAML-Common Exclusive	BRCA-All-GS	0.02	-1.53	-2.41	-1.82	4.19
BRCA-All-GS Exclusive	EAML-Common	0.01	-0.47	-1.22	-1.23	-1.98
EAML-Common Exclusive	BRCA-All-GS Exclusive	0.02	-1.42	-2.58	-2.14	4.70
BRCA-All-GS Exclusive	EAML-Common Exclusive	0.01	-1.50	-1.73	-1.66	-3.01
EAML-Common Exclusive	Overlap	0.00	-0.20	-0.27	-0.47	-0.24
BRCA-All-GS Exclusive	Overlap	0.00	14.35	6.76	15.58	7.27
Overlap	Exclusives	0.04	2.56	4.52	2.65	9.34

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	 
EAML-Common Exclusive	262	259	LOC100129083;C9orf47;SERPINA3
BRCA-All-GS Exclusive	256	256	
Overlap	6	6