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)
WaveAF1 Exclusive	BRCA-rare-q01	2.44e-06	1.37e-08	3.93e-76	9.84e-64
BRCA-rare-q01 Exclusive	WaveAF1	5.45e-05	2.90e-04	8.70e-55	2.29e-46
WaveAF1 Exclusive	BRCA-rare-q01 Exclusive	1.13e-05	7.31e-08	2.35e-63	1.56e-50
BRCA-rare-q01 Exclusive	WaveAF1 Exclusive	1.10e-04	1.20e-03	4.26e-45	5.04e-31
WaveAF1 Exclusive	Overlap	6.82e-02	1.56e-02	4.64e-17	4.00e-17
BRCA-rare-q01 Exclusive	Overlap	1.39e-02	9.06e-02	6.38e-18	6.82e-17
Overlap	Exclusives	5.21e-08	1.35e-08	2.06e-107	4.12e-71



Evaluating how well WaveAF1 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)
WaveAF1 Exclusive	BRCA-rare-q01	0.85	3.65	7.53	5.98	20.22
BRCA-rare-q01 Exclusive	WaveAF1	0.84	3.08	6.46	6.19	16.32
WaveAF1 Exclusive	BRCA-rare-q01 Exclusive	0.84	3.85	7.30	5.70	17.20
BRCA-rare-q01 Exclusive	WaveAF1 Exclusive	0.81	3.13	5.62	7.25	12.16
WaveAF1 Exclusive	Overlap	0.90	1.64	2.56	4.04	10.23
BRCA-rare-q01 Exclusive	Overlap	0.91	1.72	3.89	4.56	8.38
Overlap	Exclusives	0.81	2.92	7.58	7.84	22.48

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)
WaveAF1 Exclusive	BRCA-rare-q01	0.09	3.29	9.42	20.10	73.08
BRCA-rare-q01 Exclusive	WaveAF1	0.05	2.60	7.87	12.74	38.19
WaveAF1 Exclusive	BRCA-rare-q01 Exclusive	0.06	3.86	10.54	14.35	56.51
BRCA-rare-q01 Exclusive	WaveAF1 Exclusive	0.03	5.35	6.91	12.12	20.11
WaveAF1 Exclusive	Overlap	0.04	1.72	3.80	18.18	107.58
BRCA-rare-q01 Exclusive	Overlap	0.03	-0.55	6.49	11.38	41.33
Overlap	Exclusives	0.07	3.25	8.35	23.31	73.13

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	 
WaveAF1 Exclusive	129	129	
BRCA-rare-q01 Exclusive	186	185	CHD2
Overlap	36	36