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)
Justin PD	Shima PD	7.29e-19	8.40e-01	2.05e-07	1.92e-05
Shima PD	Justin PD	3.03e-01	5.97e-01	1.78e-05	3.03e-05



Evaluating how well Justin PD genes are linked to Shima PD 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)
Justin PD	Shima PD	0.60	-3.24	-0.73	-1.15	3.99
Shima PD	Justin PD	0.65	0.36	-0.00	0.49	3.90

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)
Justin PD	Shima PD	0.01	-1.74	-0.29	-0.48	2.79
Shima PD	Justin PD	0.00	0.05	-0.65	-0.08	0.41

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	 
Justin PD	57	57	
Shima PD	161	160	9-Sep