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)
pph2 Exclusive	magma	1.02e-01	7.80e-01	2.09e-03	2.51e-01
magma Exclusive	pph2	5.25e-01	9.64e-03	5.21e-02	6.46e-41
pph2 Exclusive	magma Exclusive	1.23e-01	7.60e-01	1.16e-03	5.02e-01
magma Exclusive	pph2 Exclusive	4.71e-01	8.99e-03	1.35e-01	1.51e-40
pph2 Exclusive	Overlap	9.92e-02	9.92e-02	9.92e-02	1.25e-01
magma Exclusive	Overlap	9.92e-02	9.92e-02	9.92e-02	1.05e-01
Overlap	Exclusives	3.13e-01	1.36e-07	2.35e-58	5.40e-37



Evaluating how well pph2 genes are linked to magma 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)
pph2 Exclusive	magma	0.57	1.97	0.41	0.24	1.21
magma Exclusive	pph2	0.75	-0.05	5.32	0.11	11.69
pph2 Exclusive	magma Exclusive	0.55	1.51	0.48	0.40	0.90
magma Exclusive	pph2 Exclusive	0.75	-0.14	4.81	0.04	12.68
pph2 Exclusive	Overlap	0.97	2.54	-3.94	0.79	1.76
magma Exclusive	Overlap	1.00	1.55	5.14	1.66	1.78
Overlap	Exclusives	0.75	-12.91	6.20	0.72	14.65

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)
pph2 Exclusive	magma	0.00	3.84	-0.65	0.30	0.67
magma Exclusive	pph2	0.02	-0.29	6.13	0.21	11.54
pph2 Exclusive	magma Exclusive	0.00	2.58	0.01	0.06	-0.04
magma Exclusive	pph2 Exclusive	0.02	-0.47	5.19	0.01	13.49
pph2 Exclusive	Overlap	0.00	4.74	-2.03	0.43	1.29
magma Exclusive	Overlap	0.01	19.84	242.70	18.91	8.33
Overlap	Exclusives	0.03	-1.77	8.59	0.64	17.67

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	 
pph2 Exclusive	195	195	
magma Exclusive	30	28	KIAA1751;MICA
Overlap	1	1