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)
dea Exclusive	gwas2	2.86e-02	1.13e-02	6.18e-04	4.44e-03
gwas2 Exclusive	dea	4.21e-01	4.18e-01	5.83e-01	1.08e-02
dea Exclusive	gwas2 Exclusive	3.50e-02	6.11e-03	2.10e-03	5.77e-03
gwas2 Exclusive	dea Exclusive	3.47e-01	3.69e-01	6.97e-01	4.66e-02
dea Exclusive	Overlap	1.12e-01	9.92e-02	1.05e-01	1.33e-01
gwas2 Exclusive	Overlap	9.92e-02	9.92e-02	9.92e-02	9.92e-02
Overlap	Exclusives	1.41e-09	9.30e-09	3.90e-21	8.87e-11



Evaluating how well dea genes are linked to gwas2 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)
dea Exclusive	gwas2	0.63	1.64	2.46	1.34	2.51
gwas2 Exclusive	dea	0.67	1.23	0.98	0.96	2.85
dea Exclusive	gwas2 Exclusive	0.62	1.36	2.93	1.11	2.60
gwas2 Exclusive	dea Exclusive	0.65	1.10	0.80	0.62	2.29
dea Exclusive	Overlap	0.96	1.37	3.23	1.58	1.66
gwas2 Exclusive	Overlap	1.00	1.76	4.14	1.76	1.68
Overlap	Exclusives	0.78	5.08	6.97	3.06	6.87

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)
dea Exclusive	gwas2	0.00	1.00	2.31	0.72	1.87
gwas2 Exclusive	dea	0.00	4.67	7.35	4.69	4.52
dea Exclusive	gwas2 Exclusive	0.00	0.96	3.02	0.71	0.86
gwas2 Exclusive	dea Exclusive	0.00	1.14	1.05	0.78	0.53
dea Exclusive	Overlap	0.00	1.79	10.63	2.14	2.37
gwas2 Exclusive	Overlap	0.01	50.11	455.12	71.40	64.92
Overlap	Exclusives	0.02	32.07	15.91	9.51	20.67

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	 
dea Exclusive	18	18	
gwas2 Exclusive	38	37	HLA
Overlap	1	1