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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