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)
EPI Exclusive	tier2	1.41e-08	1.11e-06	7.71e-32	4.49e-18
tier2 Exclusive	EPI	2.45e-15	1.03e-12	9.19e-48	7.24e-48
EPI Exclusive	tier2 Exclusive	5.05e-05	1.81e-04	5.62e-24	3.62e-13
tier2 Exclusive	EPI Exclusive	4.97e-14	1.21e-11	4.11e-45	1.89e-46
EPI Exclusive	Overlap	8.54e-06	2.65e-05	1.41e-09	6.52e-07
tier2 Exclusive	Overlap	6.15e-02	9.29e-02	3.10e-03	1.83e-02
Overlap	Exclusives	1.20e-24	4.19e-28	3.97e-48	5.33e-63



Evaluating how well EPI genes are linked to tier2 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)
EPI Exclusive	tier2	0.76	8.91	9.37	8.10	11.10
tier2 Exclusive	EPI	0.73	5.24	8.67	5.78	16.30
EPI Exclusive	tier2 Exclusive	0.74	6.94	6.69	6.17	8.38
tier2 Exclusive	EPI Exclusive	0.73	5.03	8.20	5.85	16.72
EPI Exclusive	Overlap	0.87	8.87	6.41	6.51	5.83
tier2 Exclusive	Overlap	0.69	3.31	2.45	2.01	3.10
Overlap	Exclusives	0.74	5.69	15.39	5.36	18.84

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)
EPI Exclusive	tier2	0.03	21.65	15.57	22.47	27.20
tier2 Exclusive	EPI	0.09	7.13	22.82	18.47	54.99
EPI Exclusive	tier2 Exclusive	0.02	12.20	8.34	12.88	12.26
tier2 Exclusive	EPI Exclusive	0.09	6.60	23.78	16.75	65.45
EPI Exclusive	Overlap	0.02	48.03	22.27	38.68	42.81
tier2 Exclusive	Overlap	0.00	2.27	3.96	2.16	2.97
Overlap	Exclusives	0.08	10.98	37.95	12.46	41.23

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	 
EPI Exclusive	428	424	FPGT.TNNI3K.TNNI3K.FPGT.TNNI3K;OR4N4;SIGLEC5;HLA.A
tier2 Exclusive	126	120	HMGN2P46;9-Sep;CHD2;6-Sep;MALAT1;5-Sep
Overlap	21	21