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)
WaveAF001 Exclusive	BRCA-rare-q01	3.43e-08	5.68e-07	5.31e-84	1.03e-63
BRCA-rare-q01 Exclusive	WaveAF001	6.04e-07	5.76e-04	1.86e-50	2.00e-41
WaveAF001 Exclusive	BRCA-rare-q01 Exclusive	1.23e-08	8.65e-07	3.08e-66	1.06e-49
BRCA-rare-q01 Exclusive	WaveAF001 Exclusive	1.54e-05	1.99e-03	1.54e-33	2.20e-26
WaveAF001 Exclusive	Overlap	6.64e-02	3.56e-02	7.98e-20	3.84e-18
BRCA-rare-q01 Exclusive	Overlap	1.76e-02	2.37e-02	5.18e-19	1.66e-18
Overlap	Exclusives	7.84e-07	2.79e-07	3.91e-83	5.45e-57



Evaluating how well WaveAF001 genes are linked to BRCA-rare-q01 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)
WaveAF001 Exclusive	BRCA-rare-q01	0.85	3.57	5.49	5.98	18.14
BRCA-rare-q01 Exclusive	WaveAF001	0.88	3.96	6.89	6.45	15.61
WaveAF001 Exclusive	BRCA-rare-q01 Exclusive	0.84	3.48	5.93	6.60	14.56
BRCA-rare-q01 Exclusive	WaveAF001 Exclusive	0.86	1.71	5.77	5.63	12.96
WaveAF001 Exclusive	Overlap	0.87	2.25	2.98	3.71	8.58
BRCA-rare-q01 Exclusive	Overlap	0.91	4.61	6.03	4.19	9.14
Overlap	Exclusives	0.81	2.09	6.14	5.62	17.55

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)
WaveAF001 Exclusive	BRCA-rare-q01	0.09	2.80	8.53	21.11	82.24
BRCA-rare-q01 Exclusive	WaveAF001	0.09	3.33	9.14	19.10	113.14
WaveAF001 Exclusive	BRCA-rare-q01 Exclusive	0.06	4.33	8.41	20.48	44.34
BRCA-rare-q01 Exclusive	WaveAF001 Exclusive	0.05	3.29	8.64	18.51	83.58
WaveAF001 Exclusive	Overlap	0.03	-0.26	3.62	13.33	53.69
BRCA-rare-q01 Exclusive	Overlap	0.06	1.90	8.24	14.76	158.31
Overlap	Exclusives	0.06	2.84	7.92	15.58	48.26

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	 
WaveAF001 Exclusive	92	92	
BRCA-rare-q01 Exclusive	181	180	CHD2
Overlap	41	41