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)
AllVar2MethodGenes Exclusive	TCGA	2.22e-12	1.11e-10	9.68e-15	3.88e-18
TCGA Exclusive	AllVar2MethodGenes	5.16e-05	6.94e-04	2.60e-07	2.68e-04
AllVar2MethodGenes Exclusive	TCGA Exclusive	5.31e-09	1.08e-07	7.36e-11	6.55e-15
TCGA Exclusive	AllVar2MethodGenes Exclusive	3.07e-03	1.58e-02	5.90e-05	1.32e-02
AllVar2MethodGenes Exclusive	Overlap	3.30e-07	3.30e-07	3.30e-07	3.45e-07
TCGA Exclusive	Overlap	3.30e-07	3.30e-07	3.30e-07	4.12e-07
Overlap	Exclusives	2.45e-12	1.38e-10	3.69e-17	2.53e-14



Evaluating how well AllVar2MethodGenes genes are linked to TCGA 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)
AllVar2MethodGenes Exclusive	TCGA	0.88	2.96	6.97	3.59	11.37
TCGA Exclusive	AllVar2MethodGenes	0.60	2.58	3.31	1.95	3.86
AllVar2MethodGenes Exclusive	TCGA Exclusive	0.86	3.63	6.30	3.77	9.28
TCGA Exclusive	AllVar2MethodGenes Exclusive	0.58	2.08	2.65	1.66	3.07
AllVar2MethodGenes Exclusive	Overlap	1.00	2.18	4.00	1.94	5.00
TCGA Exclusive	Overlap	1.00	1.66	3.37	2.22	4.88
Overlap	Exclusives	0.67	3.21	5.72	2.88	8.10

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)
AllVar2MethodGenes Exclusive	TCGA	0.07	20.46	56.39	27.66	186.77
TCGA Exclusive	AllVar2MethodGenes	0.05	39.13	56.79	37.70	61.89
AllVar2MethodGenes Exclusive	TCGA Exclusive	0.04	17.16	34.02	21.44	77.72
TCGA Exclusive	AllVar2MethodGenes Exclusive	0.03	26.72	30.79	18.62	31.91
AllVar2MethodGenes Exclusive	Overlap	0.07	48.41	188.10	26.98	140.45
TCGA Exclusive	Overlap	0.10	17.29	178.92	99.15	115.66
Overlap	Exclusives	0.06	34.45	59.38	27.08	53.49

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	 
AllVar2MethodGenes Exclusive	130	127	;GPR75-ASB3;DKK 3.00
TCGA Exclusive	51	51	
Overlap	7	7