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Table 3 Performances of Scuba and of some gene prioritization web tools in the unbiased setting of Börnigen et al. [20]

From: Scuba: scalable kernel-based gene prioritization

Tool/Method Response Rank Rank TPR in top TPR in top TPR in top AUC
  rate (%) median average 5% (%) 10% (%) 30% (%)  
Genome-wide prioritization methods  
Scuba 100 10.55 20.48 ± 23.53 33.3 47.6 78.6 0.80
Candid [44] 100 18.10 27.35 ± 24.62 21.4 33.3 64.3 0.73
Endeavour [39] 100 15.49 21.47 ± 22.37 28.6 38.1 71.4 0.79
Pinta [41] 100 19.03 23.52 ± 23.58 26.2 31.0 71.4 0.77
Candidate set-based prioritization methods  
Scuba 100 12.95 23.32 ± 25.46 28.6 45.2 73.8 0.78
Suspects [45] 88.9a 12.77a 24.64 ± 26.42a 33.3a 33.3a 63.0a 0.76a
ToppGene [40] 97.6 16.80 34.53 ± 35.31 35.7 42.9 52.4 0.66
GeneWanderer-RW [43] 88.1 22.10 29.55 ± 26.28 16.7 26.2 61.9 0.71
Posmed-KS [46] 47.6 31.44 42.07 ± 30.98 4.7 7.1 23.8 0.58
GeneDistiller [38] 97.6 11.11 15.37 ± 13.77 26.2 47.6 78.6 0.85
Endeavour [39] 100 11.16 18.41 ± 21.39 26.2 42.9 90.5 0.82
Pinta [41] 100 18.87 25.23 ± 24.72 28.6 31.0 71.4 0.75
  1. Response rate is the percentage of gene-disease associations considered by each tool. Values for Suspects were computed on the first 27 associations only (highlighted by a)
  2. Italics indicates the top ranking score of each column