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)
RareAndCommon_ComboConsensus Exclusive	BRCA-familial	9.08e-09	3.84e-08	4.48e-30	7.99e-28
BRCA-familial Exclusive	RareAndCommon_ComboConsensus	2.03e-05	9.73e-05	1.45e-36	1.34e-38
RareAndCommon_ComboConsensus Exclusive	BRCA-familial Exclusive	3.38e-07	4.71e-07	9.86e-19	5.53e-20
BRCA-familial Exclusive	RareAndCommon_ComboConsensus Exclusive	8.69e-05	5.55e-04	6.14e-36	1.84e-36
RareAndCommon_ComboConsensus Exclusive	Overlap	4.43e-04	2.45e-03	1.18e-16	3.09e-10
BRCA-familial Exclusive	Overlap	2.64e-09	8.79e-07	1.18e-16	1.37e-11
Overlap	Exclusives	5.93e-11	5.66e-07	8.71e-69	1.14e-32



Evaluating how well RareAndCommon_ComboConsensus genes are linked to BRCA-familial 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)
RareAndCommon_ComboConsensus Exclusive	BRCA-familial	0.98	3.34	5.89	2.79	7.50
BRCA-familial Exclusive	RareAndCommon_ComboConsensus	0.71	1.36	4.71	4.25	17.04
RareAndCommon_ComboConsensus Exclusive	BRCA-familial Exclusive	0.98	3.23	5.44	3.23	5.62
BRCA-familial Exclusive	RareAndCommon_ComboConsensus Exclusive	0.71	1.18	5.45	3.92	14.53
RareAndCommon_ComboConsensus Exclusive	Overlap	0.99	3.01	3.87	2.30	4.53
BRCA-familial Exclusive	Overlap	0.99	1.94	4.00	3.00	4.50
Overlap	Exclusives	0.72	2.42	5.33	2.45	14.81

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)
RareAndCommon_ComboConsensus Exclusive	BRCA-familial	0.10	3.23	28.47	13.74	117.69
BRCA-familial Exclusive	RareAndCommon_ComboConsensus	0.06	4.01	17.05	16.18	42.11
RareAndCommon_ComboConsensus Exclusive	BRCA-familial Exclusive	0.09	1.86	60.57	8.71	219.71
BRCA-familial Exclusive	RareAndCommon_ComboConsensus Exclusive	0.05	3.26	14.64	12.90	39.07
RareAndCommon_ComboConsensus Exclusive	Overlap	0.03	4.95	13.36	14.09	127.20
BRCA-familial Exclusive	Overlap	0.06	10.11	137.38	87.73	227.45
Overlap	Exclusives	0.06	5.54	21.27	11.21	41.35

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	 
RareAndCommon_ComboConsensus Exclusive	384	382	;PRAMEF11
BRCA-familial Exclusive	16	16	
Overlap	7	7