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)
Rare2MethodGenes-q0-01 Exclusive	TCGA	7.70e-11	2.66e-09	1.45e-13	7.39e-18
TCGA Exclusive	Rare2MethodGenes-q0-01	1.07e-02	2.96e-02	1.77e-03	2.03e-04
Rare2MethodGenes-q0-01 Exclusive	TCGA Exclusive	2.70e-08	2.99e-08	1.58e-11	6.71e-13
TCGA Exclusive	Rare2MethodGenes-q0-01 Exclusive	1.94e-01	1.19e-01	6.21e-03	9.04e-04
Rare2MethodGenes-q0-01 Exclusive	Overlap	7.62e-07	2.82e-05	4.31e-07	4.12e-07
TCGA Exclusive	Overlap	3.30e-07	3.30e-07	3.30e-07	3.77e-07
Overlap	Exclusives	7.00e-13	6.69e-09	3.64e-31	1.11e-13



Evaluating how well Rare2MethodGenes-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)
Rare2MethodGenes-q0-01 Exclusive	TCGA	0.85	2.66	6.29	2.63	8.97
TCGA Exclusive	Rare2MethodGenes-q0-01	0.65	2.55	2.53	2.33	4.85
Rare2MethodGenes-q0-01 Exclusive	TCGA Exclusive	0.83	2.54	6.42	2.89	7.33
TCGA Exclusive	Rare2MethodGenes-q0-01 Exclusive	0.61	2.36	2.51	1.92	3.66
Rare2MethodGenes-q0-01 Exclusive	Overlap	0.99	1.45	4.14	1.88	4.24
TCGA Exclusive	Overlap	1.00	1.61	3.70	2.39	4.56
Overlap	Exclusives	0.73	2.86	5.49	3.36	9.42

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)
Rare2MethodGenes-q0-01 Exclusive	TCGA	0.04	10.34	42.16	13.49	72.92
TCGA Exclusive	Rare2MethodGenes-q0-01	0.04	7.66	44.80	45.96	53.90
Rare2MethodGenes-q0-01 Exclusive	TCGA Exclusive	0.02	10.25	34.78	11.28	7.25
TCGA Exclusive	Rare2MethodGenes-q0-01 Exclusive	0.02	41.75	26.55	33.14	32.33
Rare2MethodGenes-q0-01 Exclusive	Overlap	0.02	4.09	30.60	9.45	51.85
TCGA Exclusive	Overlap	0.07	1.93	114.67	75.39	221.54
Overlap	Exclusives	0.06	31.31	49.05	24.58	46.90

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	 
Rare2MethodGenes-q0-01 Exclusive	85	82	;C4B_2;SSPO
TCGA Exclusive	51	51	
Overlap	7	7