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	1.99e-01	1.14e-02	3.31e-05	1.27e-05
BRCA-All-GS Exclusive	EAML-Common	6.17e-04	5.49e-01	3.23e-03	9.90e-02
EAML-Common Exclusive	BRCA-All-GS Exclusive	2.03e-01	1.34e-02	1.02e-04	1.04e-05
BRCA-All-GS Exclusive	EAML-Common Exclusive	5.96e-04	5.95e-01	8.23e-03	6.06e-02
EAML-Common Exclusive	Overlap	2.35e-01	6.84e-02	1.74e-01	3.58e-01
BRCA-All-GS Exclusive	Overlap	3.44e-01	4.41e-01	2.01e-01	6.14e-01
Overlap	Exclusives	8.76e-03	8.96e-02	3.24e-04	4.84e-13



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	-0.90	-2.79	-2.07	5.53
BRCA-All-GS Exclusive	EAML-Common	0.45	-2.03	-1.56	-1.45	-2.38
EAML-Common Exclusive	BRCA-All-GS Exclusive	0.59	-0.92	-2.50	-1.84	4.82
BRCA-All-GS Exclusive	EAML-Common Exclusive	0.44	-1.96	-1.93	-1.94	-2.74
EAML-Common Exclusive	Overlap	0.43	-0.85	-1.34	-0.72	-0.35
BRCA-All-GS Exclusive	Overlap	0.65	-0.30	0.77	1.11	1.01
Overlap	Exclusives	0.61	0.88	1.83	0.87	7.23

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	-0.98	-2.78	-1.60	3.04
BRCA-All-GS Exclusive	EAML-Common	0.01	-0.67	-0.60	-0.73	-1.23
EAML-Common Exclusive	BRCA-All-GS Exclusive	0.02	-0.96	-2.92	-1.49	3.15
BRCA-All-GS Exclusive	EAML-Common Exclusive	0.01	-0.47	-1.53	-0.88	-1.54
EAML-Common Exclusive	Overlap	0.00	-0.50	-0.18	-0.66	-0.20
BRCA-All-GS Exclusive	Overlap	0.00	23.16	14.85	16.95	4.55
Overlap	Exclusives	0.03	1.88	4.36	1.91	11.30

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	148	147	C9orf47
BRCA-All-GS Exclusive	258	258	
Overlap	4	4