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-q0-01 Exclusive	TCGA	4.38e-13	8.03e-13	5.50e-16	2.27e-16
TCGA Exclusive	AllVar2MethodGenes-q0-01	6.14e-06	5.82e-05	3.90e-08	7.66e-06
AllVar2MethodGenes-q0-01 Exclusive	TCGA Exclusive	1.83e-09	1.03e-09	9.09e-12	7.96e-13
TCGA Exclusive	AllVar2MethodGenes-q0-01 Exclusive	9.14e-04	4.83e-03	6.12e-05	2.93e-03
AllVar2MethodGenes-q0-01 Exclusive	Overlap	3.30e-07	3.30e-07	3.30e-07	4.50e-07
TCGA Exclusive	Overlap	3.30e-07	3.30e-07	3.30e-07	3.61e-07
Overlap	Exclusives	1.72e-14	1.76e-12	5.77e-20	1.71e-18



Evaluating how well AllVar2MethodGenes-q0-01 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-q0-01 Exclusive	TCGA	0.86	2.65	6.90	2.84	9.05
TCGA Exclusive	AllVar2MethodGenes-q0-01	0.68	2.18	3.15	1.93	5.94
AllVar2MethodGenes-q0-01 Exclusive	TCGA Exclusive	0.84	3.01	6.17	2.79	8.19
TCGA Exclusive	AllVar2MethodGenes-q0-01 Exclusive	0.64	2.10	2.53	1.63	4.55
AllVar2MethodGenes-q0-01 Exclusive	Overlap	1.00	2.44	4.83	2.20	4.40
TCGA Exclusive	Overlap	1.00	1.64	3.66	2.01	4.59
Overlap	Exclusives	0.75	3.22	6.61	2.79	9.29

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-q0-01 Exclusive	TCGA	0.07	21.03	84.23	37.58	162.03
TCGA Exclusive	AllVar2MethodGenes-q0-01	0.06	42.83	88.68	61.67	109.07
AllVar2MethodGenes-q0-01 Exclusive	TCGA Exclusive	0.04	19.04	54.55	26.60	62.91
TCGA Exclusive	AllVar2MethodGenes-q0-01 Exclusive	0.03	32.09	56.28	42.51	58.34
AllVar2MethodGenes-q0-01 Exclusive	Overlap	0.06	84.85	218.85	78.50	16.08
TCGA Exclusive	Overlap	0.10	9.27	232.06	62.52	78.09
Overlap	Exclusives	0.07	44.00	68.43	38.44	58.09

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-q0-01 Exclusive	70	69	
TCGA Exclusive	51	51	
Overlap	7	7