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	Tier2-T2D	8.15e-01	7.47e-01	7.21e-01	3.01e-01
Tier2-T2D Exclusive	EPI_FDR001	6.53e-01	5.21e-01	1.76e-01	8.17e-01
EPI_FDR001 Exclusive	Tier2-T2D Exclusive	8.72e-01	6.63e-01	9.78e-01	5.58e-01
Tier2-T2D Exclusive	EPI_FDR001 Exclusive	9.64e-01	6.55e-01	2.92e-01	8.27e-01
EPI_FDR001 Exclusive	Overlap	2.41e-01	1.33e-01	2.86e-01	4.99e-01
Tier2-T2D Exclusive	Overlap	1.02e-02	1.02e-02	1.02e-02	1.10e-02
Overlap	Exclusives	3.85e-02	1.07e-01	1.14e-02	3.55e-01



Evaluating how well EPI_FDR001 genes are linked to Tier2-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	Tier2-T2D	0.55	-0.24	-0.35	-0.25	0.79
Tier2-T2D Exclusive	EPI_FDR001	0.51	1.14	0.97	1.00	0.21
EPI_FDR001 Exclusive	Tier2-T2D Exclusive	0.59	0.51	0.58	0.41	1.16
Tier2-T2D Exclusive	EPI_FDR001 Exclusive	0.49	0.58	0.46	0.14	-0.25
EPI_FDR001 Exclusive	Overlap	0.43	-1.22	-1.48	-1.02	-0.45
Tier2-T2D Exclusive	Overlap	0.88	2.53	2.61	2.90	2.58
Overlap	Exclusives	0.54	1.24	2.19	1.46	1.33

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	Tier2-T2D	0.00	-0.52	-0.80	-0.51	-0.13
Tier2-T2D Exclusive	EPI_FDR001	0.01	8.42	5.24	7.35	3.64
EPI_FDR001 Exclusive	Tier2-T2D Exclusive	0.00	-0.24	0.03	-0.25	-0.04
Tier2-T2D Exclusive	EPI_FDR001 Exclusive	0.00	0.00	-0.24	-0.28	-0.42
EPI_FDR001 Exclusive	Overlap	0.00	-0.40	-0.77	-0.39	-0.36
Tier2-T2D Exclusive	Overlap	0.04	81.26	261.85	63.82	36.10
Overlap	Exclusives	0.01	2.75	0.90	3.33	3.67

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
Tier2-T2D Exclusive	12	12	
Overlap	4	4