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)
GeneGroup1	GeneGroup2	3.09e-23	2.32e-30	2.72e-66	2.40e-61
GeneGroup2	GeneGroup1	1.67e-21	2.22e-19	6.17e-47	6.86e-41



Evaluating how well GeneGroup1 genes are linked to GeneGroup2 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)
GeneGroup1	GeneGroup2	0.83	9.10	13.10	10.46	19.16
GeneGroup2	GeneGroup1	0.85	10.91	11.22	10.17	14.57

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)
GeneGroup1	GeneGroup2	0.07	16.94	33.88	33.68	49.48
GeneGroup2	GeneGroup1	0.07	23.61	43.59	57.94	58.66

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	 
GeneGroup1	143	141	C3orf70;AMER1
GeneGroup2	270	264	KMT2D;MALAT1;KMT2A;KMT2C;KMT2B;RECQL4