Table 2.

Performances of Scuba, MKL1class and ProDiGe in the unbiased setting of Börnigen et al. [20]

Tool/Method	Rank	Rank	TPR in top	TPR in top	TPR in top	AUC	Rank difference
	median	average	5% (%)	10% (%)	30% (%)		p-value
Genome-wide prioritization methods
Scuba	10.55	20.48 ± 23.53	33.3	47.6	78.6	0.80	-
MKL1class [12]	13.30	23.42 ± 23.23	21.4	47.6	69.0	0.77	2.5 ·10−2 *
ProDiGe [13]	11.73	24.45 ± 27.33	31.0	45.2	71.4	0.76	3.0 ·10−7 *
Candidate set-based prioritization methods
Scuba	12.95	23.32 ± 25.46	28.6	45.2	73.8	0.78	-
MKL1class [12]	15.07	25.63 ± 24.73	23.8	40.5	61.9	0.76	9.7 ·10−2
ProDiGe [13]	14.41	26.39 ± 29.09	26.2	40.5	71.4	0.75	2.7 ·10−3 *

Values refer to predictions on all the 42 gene-disease associations. Rank difference p-values were obtained using Wilcoxon signed rank tests comparing separately Scuba/MKL1class and Scuba/ProDiGe ranks differences. Asterisks indicate significance of the tests at a threshold of 0.05

Italics indicates the top ranking score of each column