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)
Common2MethodGenes-q0-01 Exclusive	TCGA	2.65e-12	9.92e-12	1.38e-16	3.75e-16
TCGA Exclusive	Common2MethodGenes-q0-01	1.02e-04	8.82e-04	6.05e-06	4.52e-05
Common2MethodGenes-q0-01 Exclusive	TCGA Exclusive	2.42e-09	8.53e-09	8.76e-13	8.85e-14
TCGA Exclusive	Common2MethodGenes-q0-01 Exclusive	2.35e-02	7.28e-02	9.20e-05	3.02e-03
Common2MethodGenes-q0-01 Exclusive	Overlap	2.62e-06	2.62e-06	2.62e-06	3.28e-06
TCGA Exclusive	Overlap	2.62e-06	2.62e-06	2.62e-06	2.74e-06
Overlap	Exclusives	1.40e-13	1.20e-12	5.31e-20	6.22e-19



Evaluating how well Common2MethodGenes-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)
Common2MethodGenes-q0-01 Exclusive	TCGA	0.87	2.81	8.20	3.22	8.95
TCGA Exclusive	Common2MethodGenes-q0-01	0.71	2.59	2.77	2.02	5.65
Common2MethodGenes-q0-01 Exclusive	TCGA Exclusive	0.85	2.99	7.31	3.06	8.65
TCGA Exclusive	Common2MethodGenes-q0-01 Exclusive	0.67	2.73	2.84	2.03	4.26
Common2MethodGenes-q0-01 Exclusive	Overlap	1.00	2.06	3.98	2.35	4.75
TCGA Exclusive	Overlap	1.00	1.70	3.04	2.20	4.29
Overlap	Exclusives	0.77	2.45	5.25	2.53	9.53

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)
Common2MethodGenes-q0-01 Exclusive	TCGA	0.05	15.00	64.44	27.97	78.91
TCGA Exclusive	Common2MethodGenes-q0-01	0.07	29.20	91.08	68.32	113.74
Common2MethodGenes-q0-01 Exclusive	TCGA Exclusive	0.03	12.13	41.85	17.18	13.00
TCGA Exclusive	Common2MethodGenes-q0-01 Exclusive	0.04	82.88	45.64	59.22	93.74
Common2MethodGenes-q0-01 Exclusive	Overlap	0.03	22.51	137.19	35.90	115.47
TCGA Exclusive	Overlap	0.10	18.58	191.08	92.80	213.79
Overlap	Exclusives	0.07	38.63	56.81	27.40	51.92

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	 
Common2MethodGenes-q0-01 Exclusive	47	46	
TCGA Exclusive	52	52	
Overlap	6	6