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-gwas	2.70e-01	4.63e-01	1.48e-05	9.82e-06
BRCA-gwas Exclusive	RareAndCommon_2methodConsensus	3.48e-01	9.79e-01	8.14e-05	1.17e-03
RareAndCommon_2methodConsensus Exclusive	BRCA-gwas Exclusive	2.57e-01	4.15e-01	1.66e-05	3.10e-05
BRCA-gwas Exclusive	RareAndCommon_2methodConsensus Exclusive	3.57e-01	9.96e-01	4.76e-04	1.69e-03
RareAndCommon_2methodConsensus Exclusive	Overlap	2.83e-01	4.31e-01	7.31e-02	6.83e-02
BRCA-gwas Exclusive	Overlap	2.60e-01	4.75e-01	6.99e-02	1.86e-02
Overlap	Exclusives	3.68e-01	6.94e-02	1.71e-41	2.74e-09



Evaluating how well RareAndCommon_2methodConsensus genes are linked to BRCA-gwas 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-gwas	0.61	-0.38	-0.00	0.88	4.56
BRCA-gwas Exclusive	RareAndCommon_2methodConsensus	0.60	-0.82	0.21	0.76	4.26
RareAndCommon_2methodConsensus Exclusive	BRCA-gwas Exclusive	0.60	-0.48	-0.16	0.74	4.41
BRCA-gwas Exclusive	RareAndCommon_2methodConsensus Exclusive	0.59	-1.17	0.08	0.50	3.56
RareAndCommon_2methodConsensus Exclusive	Overlap	0.78	-0.28	-0.18	0.13	2.70
BRCA-gwas Exclusive	Overlap	0.85	0.56	1.29	1.03	3.64
Overlap	Exclusives	0.62	1.58	2.15	1.37	7.33

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-gwas	0.02	2.00	2.92	5.68	10.37
BRCA-gwas Exclusive	RareAndCommon_2methodConsensus	0.01	0.70	2.13	4.44	5.30
RareAndCommon_2methodConsensus Exclusive	BRCA-gwas Exclusive	0.02	0.90	1.17	3.96	7.17
BRCA-gwas Exclusive	RareAndCommon_2methodConsensus Exclusive	0.01	0.68	2.13	4.02	4.20
RareAndCommon_2methodConsensus Exclusive	Overlap	0.02	12.41	14.29	30.08	4.56
BRCA-gwas Exclusive	Overlap	0.00	-0.04	0.53	2.63	8.51
Overlap	Exclusives	0.02	1.44	3.59	2.46	8.22

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	142	141	PRAMEF11
BRCA-gwas Exclusive	167	167	
Overlap	6	6