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)
EAW-FDR01 Exclusive	Tier1-T2D	9.11e-01	4.58e-01	1.56e-02	3.62e-02
Tier1-T2D Exclusive	EAW-FDR01	9.45e-02	6.44e-02	2.76e-05	2.42e-30
EAW-FDR01 Exclusive	Tier1-T2D Exclusive	8.57e-01	6.17e-01	2.62e-02	5.15e-02
Tier1-T2D Exclusive	EAW-FDR01 Exclusive	4.57e-02	9.61e-02	3.78e-06	1.44e-29
EAW-FDR01 Exclusive	Overlap	7.92e-01	8.04e-01	7.09e-02	5.93e-01
Tier1-T2D Exclusive	Overlap	3.62e-01	4.52e-01	1.91e-01	3.94e-01
Overlap	Exclusives	2.10e-05	8.53e-01	6.62e-10	4.92e-30



Evaluating how well EAW-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)
EAW-FDR01 Exclusive	Tier1-T2D	0.64	0.92	0.58	1.05	1.62
Tier1-T2D Exclusive	EAW-FDR01	0.68	-0.11	1.42	0.08	10.48
EAW-FDR01 Exclusive	Tier1-T2D Exclusive	0.65	0.66	0.58	0.89	1.65
Tier1-T2D Exclusive	EAW-FDR01 Exclusive	0.68	-0.37	1.05	-0.00	10.20
EAW-FDR01 Exclusive	Overlap	0.55	0.29	0.05	0.64	0.12
Tier1-T2D Exclusive	Overlap	0.80	1.37	1.54	1.73	1.44
Overlap	Exclusives	0.72	1.35	-0.58	1.02	12.31

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)
EAW-FDR01 Exclusive	Tier1-T2D	0.00	1.39	0.04	1.05	0.76
Tier1-T2D Exclusive	EAW-FDR01	0.02	0.41	1.18	0.53	10.13
EAW-FDR01 Exclusive	Tier1-T2D Exclusive	0.00	0.84	0.02	0.93	0.24
Tier1-T2D Exclusive	EAW-FDR01 Exclusive	0.02	-0.11	0.49	0.24	7.51
EAW-FDR01 Exclusive	Overlap	0.00	-0.04	-0.32	-0.09	-0.14
Tier1-T2D Exclusive	Overlap	0.03	153.55	91.85	86.17	45.06
Overlap	Exclusives	0.03	1.59	0.19	1.19	17.07

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	 
EAW-FDR01 Exclusive	265	264	SPANXB1
Tier1-T2D Exclusive	12	12	
Overlap	2	2