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)
Test Exclusive	Gold standard	2.73e-07	4.14e-06	1.38e-07	1.62e-07
Gold standard Exclusive	Test	1.63e-01	5.35e-01	3.63e-02	3.58e-02
Test Exclusive	Gold standard Exclusive	3.95e-05	4.22e-05	7.86e-06	2.20e-05
Gold standard Exclusive	Test Exclusive	4.06e-01	7.59e-01	7.59e-02	1.16e-01
Test Exclusive	Overlap	1.52e-05	8.49e-02	8.71e-06	1.74e-06
Gold standard Exclusive	Overlap	4.36e-07	4.36e-07	4.36e-07	1.74e-06
Overlap	Exclusives	2.74e-03	6.96e-03	1.48e-14	4.97e-05



Evaluating how well Test genes are linked to Gold standard 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)
Test Exclusive	Gold standard	0.83	3.13	5.52	2.95	5.83
Gold standard Exclusive	Test	0.57	2.17	1.63	1.62	2.75
Test Exclusive	Gold standard Exclusive	0.80	2.67	4.24	2.97	4.39
Gold standard Exclusive	Test Exclusive	0.56	1.58	0.96	1.29	2.50
Test Exclusive	Overlap	0.99	2.20	2.25	2.47	2.91
Gold standard Exclusive	Overlap	1.00	3.36	2.60	2.75	3.05
Overlap	Exclusives	0.62	1.45	3.45	2.25	4.19

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)
Test Exclusive	Gold standard	0.01	17.70	26.44	13.98	39.44
Gold standard Exclusive	Test	0.02	11.73	17.74	10.14	21.74
Test Exclusive	Gold standard Exclusive	0.01	10.32	19.11	14.63	16.99
Gold standard Exclusive	Test Exclusive	0.01	7.04	6.49	2.88	9.44
Test Exclusive	Overlap	0.01	6.60	8.97	14.16	33.11
Gold standard Exclusive	Overlap	0.09	249.66	212.66	290.74	83.46
Overlap	Exclusives	0.05	35.76	63.23	30.68	59.84

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	 
Test Exclusive	112	111	RFPL2
Gold standard Exclusive	22	21	HLA -DRB1
Overlap	3	3