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-q001	4.08e-04	2.65e-03	2.12e-43	9.08e-34
BRCA-rare-q001 Exclusive	WaveAF1	6.51e-04	1.70e-03	4.85e-46	9.68e-37
WaveAF1 Exclusive	BRCA-rare-q001 Exclusive	1.09e-03	9.96e-03	3.60e-35	1.03e-26
BRCA-rare-q001 Exclusive	WaveAF1 Exclusive	1.83e-03	3.69e-03	3.18e-38	1.55e-30
WaveAF1 Exclusive	Overlap	2.62e-02	1.08e-01	4.17e-13	7.32e-12
BRCA-rare-q001 Exclusive	Overlap	1.35e-01	1.84e-01	2.31e-09	2.06e-08
Overlap	Exclusives	1.12e-04	3.60e-05	5.37e-65	2.88e-48



Evaluating how well WaveAF1 genes are linked to BRCA-rare-q001 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-q001	0.85	2.50	3.72	4.66	10.88
BRCA-rare-q001 Exclusive	WaveAF1	0.82	1.75	6.56	6.18	13.66
WaveAF1 Exclusive	BRCA-rare-q001 Exclusive	0.83	2.19	3.35	4.54	14.13
BRCA-rare-q001 Exclusive	WaveAF1 Exclusive	0.81	2.09	4.97	6.36	14.20
WaveAF1 Exclusive	Overlap	0.89	0.95	1.61	2.96	6.76
BRCA-rare-q001 Exclusive	Overlap	0.89	0.34	2.08	3.79	6.72
Overlap	Exclusives	0.80	2.79	5.97	6.58	16.38

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-q001	0.07	4.66	6.31	21.59	95.43
BRCA-rare-q001 Exclusive	WaveAF1	0.04	1.34	8.06	15.72	43.42
WaveAF1 Exclusive	BRCA-rare-q001 Exclusive	0.04	3.71	5.10	14.94	81.64
BRCA-rare-q001 Exclusive	WaveAF1 Exclusive	0.03	2.15	5.64	13.53	24.76
WaveAF1 Exclusive	Overlap	0.04	3.68	4.52	20.68	30.74
BRCA-rare-q001 Exclusive	Overlap	0.02	-0.23	7.03	19.34	30.75
Overlap	Exclusives	0.05	2.63	6.01	19.75	42.18

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	142	142	
BRCA-rare-q001 Exclusive	96	96	
Overlap	23	23