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_2methodConsensus Exclusive	BRCA-familial	9.36e-09	1.47e-08	2.13e-16	2.91e-21
BRCA-familial Exclusive	RareAndCommon_2methodConsensus	1.34e-05	4.56e-02	3.69e-05	8.01e-04
RareAndCommon_2methodConsensus Exclusive	BRCA-familial Exclusive	7.23e-08	4.98e-08	6.35e-14	3.98e-19
BRCA-familial Exclusive	RareAndCommon_2methodConsensus Exclusive	1.58e-05	1.38e-01	4.69e-05	3.50e-03
RareAndCommon_2methodConsensus Exclusive	Overlap	4.36e-07	4.36e-07	4.36e-07	4.36e-07
BRCA-familial Exclusive	Overlap	4.36e-07	4.36e-07	4.36e-07	4.36e-06
Overlap	Exclusives	1.05e-07	7.50e-06	1.50e-25	1.19e-08



Evaluating how well RareAndCommon_2methodConsensus 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_2methodConsensus Exclusive	BRCA-familial	0.98	2.85	6.52	2.37	8.06
BRCA-familial Exclusive	RareAndCommon_2methodConsensus	0.60	-0.28	0.34	0.99	4.29
RareAndCommon_2methodConsensus Exclusive	BRCA-familial Exclusive	0.97	2.66	6.01	2.80	7.60
BRCA-familial Exclusive	RareAndCommon_2methodConsensus Exclusive	0.59	-0.45	0.22	0.78	4.10
RareAndCommon_2methodConsensus Exclusive	Overlap	1.00	1.43	2.21	1.70	3.17
BRCA-familial Exclusive	Overlap	1.00	1.26	3.07	2.05	3.09
Overlap	Exclusives	0.65	4.15	3.30	2.06	7.10

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_2methodConsensus Exclusive	BRCA-familial	0.06	8.18	27.19	18.19	111.18
BRCA-familial Exclusive	RareAndCommon_2methodConsensus	0.02	4.84	4.00	6.87	8.12
RareAndCommon_2methodConsensus Exclusive	BRCA-familial Exclusive	0.03	3.44	13.66	16.91	6.33
BRCA-familial Exclusive	RareAndCommon_2methodConsensus Exclusive	0.01	4.42	3.52	3.95	6.89
RareAndCommon_2methodConsensus Exclusive	Overlap	0.06	22.25	58.91	62.06	234.26
BRCA-familial Exclusive	Overlap	0.02	4.13	128.91	36.64	50.83
Overlap	Exclusives	0.03	27.66	25.79	11.36	26.68

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_2methodConsensus Exclusive	145	144	PRAMEF11
BRCA-familial Exclusive	20	20	
Overlap	3	3