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Table 2 Performances of Scuba, MKL1class and ProDiGe in the unbiased setting of Börnigen et al. [20]

From: Scuba: scalable kernel-based gene prioritization

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 *

  1. 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
  2. Italics indicates the top ranking score of each column