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_FDR01 Exclusive	Tier1-T2D	2.31e-02	3.79e-02	3.98e-02	1.79e-02
Tier1-T2D Exclusive	EPI_FDR01	6.76e-01	2.45e-01	3.29e-03	7.46e-01
EPI_FDR01 Exclusive	Tier1-T2D Exclusive	8.17e-02	9.79e-02	2.52e-01	2.19e-02
Tier1-T2D Exclusive	EPI_FDR01 Exclusive	7.37e-01	3.83e-01	7.93e-04	7.85e-01
EPI_FDR01 Exclusive	Overlap	1.60e-02	1.77e-02	1.55e-02	1.71e-02
Tier1-T2D Exclusive	Overlap	1.02e-02	1.02e-02	1.02e-02	1.02e-02
Overlap	Exclusives	9.11e-05	1.57e-02	8.68e-08	3.98e-02



Evaluating how well EPI_FDR01 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_FDR01 Exclusive	Tier1-T2D	0.75	2.75	3.47	2.58	3.11
Tier1-T2D Exclusive	EPI_FDR01	0.51	1.82	1.70	1.15	0.28
EPI_FDR01 Exclusive	Tier1-T2D Exclusive	0.74	2.60	2.42	2.18	2.58
Tier1-T2D Exclusive	EPI_FDR01 Exclusive	0.50	1.76	1.28	1.02	0.03
EPI_FDR01 Exclusive	Overlap	0.79	1.83	1.98	1.95	2.20
Tier1-T2D Exclusive	Overlap	0.90	3.17	2.59	2.95	2.74
Overlap	Exclusives	0.54	3.07	3.58	2.84	1.85

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_FDR01 Exclusive	Tier1-T2D	0.00	4.52	7.47	3.98	3.79
Tier1-T2D Exclusive	EPI_FDR01	0.01	6.89	6.40	3.50	4.79
EPI_FDR01 Exclusive	Tier1-T2D Exclusive	0.00	3.11	1.90	1.35	0.93
Tier1-T2D Exclusive	EPI_FDR01 Exclusive	0.01	1.77	2.38	1.77	0.95
EPI_FDR01 Exclusive	Overlap	0.00	6.45	4.09	7.59	1.77
Tier1-T2D Exclusive	Overlap	0.04	108.72	298.63	58.93	225.03
Overlap	Exclusives	0.02	7.38	2.67	6.13	5.32

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_FDR01 Exclusive	188	186	IQANK1;GCSAML-AS1
Tier1-T2D Exclusive	10	10	
Overlap	4	4