Table 3.

Average AUCs scores of gene prioritization on test set and validation set

	Performance on test set			Performance on validation set
	AUC20	AUC50	AUC100	AUC20	AUC50	AUC100
CIPHER_SP	0.0029*	0.0046*	0.0066*	0	0	0
CIPHER_DN	0.0015*	0.0027*	0.0042*	0	0	0
RWR	0.0075*	0.0178*	0.0283*	0.0233	0.0358	0.0475
DK	0.0192*	0.0255*	0.0294*	0.0211	0.0306	0.0399
RWRH	0.0916*	0.1250*	0.1664*	0.2009	0.2724	0.3288
MINProp	0.0771*	0.1266*	0.1799*	0.1963	0.2625	0.3104
BiRW	0.0421*	0.0780*	0.1142*	0.1544	0.2180	0.26672
PRINCE	0.1117	0.1468	0.2088	0.1433	0.2137	0.2715
IDLP-G	0.0040*	0.0076*	0.0166*	0.0189	0.0348	0.0519
IDLP-P	0.1051*	0.1457	0.1897	0.2003	0.2592	0.3010
IDLP	0.1123	0.1492	0.1909	0.2004	0.2572	0.2990

We compared AUCs when the number of false positive genes are up to 20, 50, 100

^*indicates IDLP significantly outperforms the baseline with p<0.05 using Student t-test