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)
epp Exclusive	ctd	1.30e-03	1.98e-01	8.71e-23	2.20e-15
ctd Exclusive	epp	1.68e-04	4.86e-02	2.09e-15	8.08e-14
epp Exclusive	ctd Exclusive	2.04e-03	1.92e-01	1.76e-21	5.52e-15
ctd Exclusive	epp Exclusive	2.08e-04	4.45e-02	2.67e-15	9.19e-14
epp Exclusive	Overlap	9.92e-02	6.11e-01	9.92e-02	9.92e-02
ctd Exclusive	Overlap	9.92e-02	9.92e-02	9.92e-02	9.92e-02
Overlap	Exclusives	8.49e-12	1.70e-15	1.05e-71	8.62e-46



Evaluating how well epp genes are linked to ctd 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)
epp Exclusive	ctd	0.78	3.03	3.21	3.30	8.68
ctd Exclusive	epp	0.74	-5.72	2.97	1.53	9.92
epp Exclusive	ctd Exclusive	0.78	2.87	2.76	3.30	7.93
ctd Exclusive	epp Exclusive	0.73	-4.51	3.34	1.70	9.55
epp Exclusive	Overlap	0.99	2.11	0.53	1.36	1.62
ctd Exclusive	Overlap	1.00	1.64	1.92	1.45	1.64
Overlap	Exclusives	0.82	3.91	11.52	2.08	14.80

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)
epp Exclusive	ctd	0.03	4.55	2.58	12.07	17.26
ctd Exclusive	epp	0.02	-0.60	11.27	9.19	26.07
epp Exclusive	ctd Exclusive	0.03	3.82	3.02	10.66	30.90
ctd Exclusive	epp Exclusive	0.02	-1.68	8.19	7.77	20.24
epp Exclusive	Overlap	0.00	15.47	-0.63	13.25	19.09
ctd Exclusive	Overlap	0.12	147.17	265.24	427.59	435.26
Overlap	Exclusives	0.05	12.51	40.37	4.45	56.70

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	 
epp Exclusive	119	118	BRD2
ctd Exclusive	102	88	MIR505;MIR3622B;CTR1B;MIR375;MIR296;MIR766;SNAR-I;CTR1C;ATP7;MIR124A-3;MIR708;MIR146A;MIR4467;MIR100
Overlap	1	1