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-FDR001 Exclusive	Tier1-T2D	5.59e-01	5.68e-01	2.63e-01	4.06e-01
Tier1-T2D Exclusive	EPI-FDR001	9.29e-01	8.41e-01	1.89e-01	8.84e-01
EPI-FDR001 Exclusive	Tier1-T2D Exclusive	6.45e-01	9.40e-01	9.15e-01	3.18e-01
Tier1-T2D Exclusive	EPI-FDR001 Exclusive	8.17e-01	9.00e-01	1.89e-01	4.88e-01
EPI-FDR001 Exclusive	Overlap	2.92e-01	1.79e-01	2.98e-01	4.90e-01
Tier1-T2D Exclusive	Overlap	1.02e-02	1.02e-02	1.02e-02	1.06e-02
Overlap	Exclusives	7.32e-02	9.88e-02	4.51e-03	4.84e-01



Evaluating how well EPI-FDR001 genes are linked to Tier1-T2D 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-FDR001 Exclusive	Tier1-T2D	0.55	-0.49	-0.45	-0.50	0.63
Tier1-T2D Exclusive	EPI-FDR001	0.50	0.52	0.58	0.19	-0.04
EPI-FDR001 Exclusive	Tier1-T2D Exclusive	0.60	0.31	0.22	0.16	1.06
Tier1-T2D Exclusive	EPI-FDR001 Exclusive	0.47	-0.08	-0.42	-0.33	-0.78
EPI-FDR001 Exclusive	Overlap	0.43	-0.99	-1.67	-1.01	-0.45
Tier1-T2D Exclusive	Overlap	0.90	3.08	3.12	2.94	2.62
Overlap	Exclusives	0.54	1.04	1.98	1.52	1.09

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-FDR001 Exclusive	Tier1-T2D	0.00	-0.65	-0.56	-0.61	-0.23
Tier1-T2D Exclusive	EPI-FDR001	0.01	7.38	5.89	1.58	5.54
EPI-FDR001 Exclusive	Tier1-T2D Exclusive	0.00	-0.27	-0.26	-0.37	-0.13
Tier1-T2D Exclusive	EPI-FDR001 Exclusive	0.00	-0.19	-0.41	-0.21	-0.31
EPI-FDR001 Exclusive	Overlap	0.00	-0.56	-0.72	-0.31	-0.50
Tier1-T2D Exclusive	Overlap	0.04	88.22	162.33	69.67	80.83
Overlap	Exclusives	0.01	2.97	0.65	1.70	2.64

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-FDR001 Exclusive	57	56	GCSAML-AS1
Tier1-T2D Exclusive	10	10	
Overlap	4	4