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)
vep_2method_RareCon_AC1 Exclusive	BRCA-Somatic	2.49e-02	2.14e-02	2.81e-08	1.11e-17
BRCA-Somatic Exclusive	vep_2method_RareCon_AC1	1.48e-02	1.89e-01	1.32e-12	1.09e-04
vep_2method_RareCon_AC1 Exclusive	BRCA-Somatic Exclusive	1.31e-01	2.64e-02	2.84e-07	7.74e-17
BRCA-Somatic Exclusive	vep_2method_RareCon_AC1 Exclusive	2.25e-02	2.57e-01	2.37e-12	3.72e-04
vep_2method_RareCon_AC1 Exclusive	Overlap	1.15e-02	1.15e-02	1.15e-02	1.15e-02
BRCA-Somatic Exclusive	Overlap	1.15e-02	2.67e-02	1.15e-02	1.15e-02
Overlap	Exclusives	2.45e-07	1.21e-05	6.39e-28	2.67e-13



Evaluating how well vep_2method_RareCon_AC1 genes are linked to BRCA-Somatic 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)
vep_2method_RareCon_AC1 Exclusive	BRCA-Somatic	0.90	1.39	3.40	2.54	8.95
BRCA-Somatic Exclusive	vep_2method_RareCon_AC1	0.62	2.37	1.95	2.21	4.91
vep_2method_RareCon_AC1 Exclusive	BRCA-Somatic Exclusive	0.90	1.10	3.13	2.20	8.56
BRCA-Somatic Exclusive	vep_2method_RareCon_AC1 Exclusive	0.61	2.30	2.21	2.22	4.44
vep_2method_RareCon_AC1 Exclusive	Overlap	1.00	1.48	3.10	1.46	2.51
BRCA-Somatic Exclusive	Overlap	1.00	1.34	1.98	1.72	2.51
Overlap	Exclusives	0.69	2.62	4.00	1.96	8.86

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)
vep_2method_RareCon_AC1 Exclusive	BRCA-Somatic	0.02	0.03	10.40	3.83	52.11
BRCA-Somatic Exclusive	vep_2method_RareCon_AC1	0.01	0.61	2.50	4.01	5.13
vep_2method_RareCon_AC1 Exclusive	BRCA-Somatic Exclusive	0.02	-0.63	7.20	2.30	35.40
BRCA-Somatic Exclusive	vep_2method_RareCon_AC1 Exclusive	0.01	0.26	1.67	2.71	4.92
vep_2method_RareCon_AC1 Exclusive	Overlap	0.03	15.44	178.41	22.52	34.39
BRCA-Somatic Exclusive	Overlap	0.01	1.77	7.76	33.46	53.43
Overlap	Exclusives	0.03	11.88	20.84	7.33	29.89

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	 
vep_2method_RareCon_AC1 Exclusive	124	123	PRAMEF11
BRCA-Somatic Exclusive	35	35	
Overlap	2	2