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	Tier2-T2D	3.95e-02	5.32e-02	8.73e-02	3.22e-02
Tier2-T2D Exclusive	EPI_FDR01	6.64e-01	1.79e-01	1.18e-02	5.99e-01
EPI_FDR01 Exclusive	Tier2-T2D Exclusive	1.33e-01	1.09e-01	2.65e-01	6.34e-02
Tier2-T2D Exclusive	EPI_FDR01 Exclusive	7.72e-01	2.51e-01	1.52e-02	8.13e-01
EPI_FDR01 Exclusive	Overlap	1.60e-02	1.71e-02	1.77e-02	1.40e-02
Tier2-T2D Exclusive	Overlap	1.02e-02	1.02e-02	1.06e-02	1.06e-02
Overlap	Exclusives	9.34e-05	7.86e-03	3.90e-06	3.02e-02



Evaluating how well EPI_FDR01 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_FDR01 Exclusive	Tier2-T2D	0.71	2.40	2.88	2.31	3.34
Tier2-T2D Exclusive	EPI_FDR01	0.51	1.88	1.99	1.62	0.44
EPI_FDR01 Exclusive	Tier2-T2D Exclusive	0.68	1.99	2.25	1.76	2.17
Tier2-T2D Exclusive	EPI_FDR01 Exclusive	0.50	1.65	1.59	1.07	0.15
EPI_FDR01 Exclusive	Overlap	0.79	1.65	1.86	1.92	2.08
Tier2-T2D Exclusive	Overlap	0.88	3.00	2.80	2.78	2.84
Overlap	Exclusives	0.54	2.80	3.82	2.99	1.98

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	Tier2-T2D	0.00	4.03	3.47	5.00	2.70
Tier2-T2D Exclusive	EPI_FDR01	0.01	4.49	5.02	5.08	3.96
EPI_FDR01 Exclusive	Tier2-T2D Exclusive	0.00	1.74	1.39	0.60	-0.06
Tier2-T2D Exclusive	EPI_FDR01 Exclusive	0.01	1.90	2.60	0.91	1.15
EPI_FDR01 Exclusive	Overlap	0.00	6.19	8.48	11.18	10.44
Tier2-T2D Exclusive	Overlap	0.04	96.49	200.87	103.96	129.59
Overlap	Exclusives	0.02	7.36	5.39	7.27	6.12

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
Tier2-T2D Exclusive	12	12	
Overlap	4	4