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Table 1 PREP-Mt performance results subdivided by gene

From: PREP-Mt: predictive RNA editor for plant mitochondrial genes

Gene No. of Species TP TN FP FN Specificity Sensitivity Accuracy Balanced Accuracy
Complex I
   nad1 10 135 1632 14 33 (2) 99.1 80.4 (98.5) 97.4 (99.1) 89.8 (98.8)
   nad2 9 140 2337 22 42 (9) 99.1 76.9 (94.0) 97.5 (98.8) 88.0 (96.5)
   nad3 22 274 1217 8 47 (4) 99.3 85.4 (98.6) 96.4 (99.2) 92.4 (99.0)
   nad4 9 133 2358 19 12 (1) 99.2 91.7 (99.3) 98.8 (99.2) 95.5 (99.2)
   nad4L 8 49 303 5 0 (0) 98.4 100.0 (100.0) 98.6 (98.6) 99.2 (99.2)
   nad5 10 122 3647 29 10 (4) 99.2 92.4 (96.8) 99.0 (99.1) 95.8 (98.0)
   nad6 10 70 995 16 15 (3) 98.4 82.4 (95.9) 97.2 (98.2) 90.4 (97.2)
   nad7 8 117 1655 5 22 (1) 99.7 84.2 (99.2) 98.5 (99.7) 91.9 (99.4)
   nad9 12 75 1236 7 5 (3) 99.4 93.8 (96.2) 99.1 (99.2) 96.6 (97.8)
Complex II
   sdh3 7 6 391 12 11 (2) 97.0 35.3 (75.0) 94.5 (96.6) 66.2 (86.0)
   sdh4 8 10 361 14 16 (3) 96.3 38.5 (76.9) 92.5 (95.6) 67.4 (86.6)
Complex III
   cob 13 117 2834 19 25 (8) 99.3 82.4 (93.6) 98.5 (99.1) 90.9 (96.5)
Complex IV
   cox1 9 38 2936 7 7 (5) 99.8 84.4 (88.4) 99.5 (99.6) 92.1 (94.1)
   cox2 19 193 2644 22 33 (11) 99.2 85.4 (94.6) 98.1 (98.9) 92.3 (96.9)
   cox3 12 80 1793 21 11 (2) 98.8 87.9 (97.6) 98.3 (98.8) 93.4 (98.2)
Complex V
   atp1 10 21 2926 10 8 (1) 99.7 72.4 (95.5) 99.4 (99.6) 86.0 (97.6)
   atp4 7 51 730 21 18 (8) 97.2 73.9 (86.4) 95.2 (96.4) 85.6 (91.8)
   atp6 12 88 1893 11 10 (2) 99.4 89.8 (97.8) 99.0 (99.3) 94.6 (98.6)
   atp8 8 16 757 10 10 (2) 98.7 61.5 (88.9) 97.5 (98.5) 80.1 (93.8)
   atp9 19 91 792 1 17 (0) 99.9 84.3 (100.0) 98.0 (99.9) 92.1 (99.9)
Cytochrome c biogenesis
   ccmB 9 216 1013 14 63 (6) 98.6 77.4 (97.3) 94.1 (98.4) 88.0 (98.0)
   ccmC 9 187 1212 24 26 (1) 98.1 87.8 (99.5) 96.5 (98.2) 92.9 (98.8)
   ccmFc 6 84 1631 23 30 (10) 98.6 73.7 (89.4) 97.0 (98.1) 86.1 (94.0)
   ccmFn 6 155 2249 39 38 (21) 98.3 80.3 (88.1) 96.9 (97.6) 89.3 (93.2)
Ribosomal proteins
   rpl2 4 2 1057 14 6 (4) 98.7 25.0 (33.3) 98.1 (98.3) 61.8 (66.0)
   rpl5 9 45 919 14 5 (3) 98.5 90.0 98.1 (98.3) 94.2 (96.1)
   rpl6 3 0 138 3 0 (0) 97.9 - 97.9 (97.9) -
   rpl16 9 33 692 6 13 (2) 99.1 71.7 (94.3) 97.4 (98.9) 85.4 (96.7)
   rps1 3 2 295 4 5 (5) 98.7 28.6 (28.6) 97.1 (97.1) 63.6 (63.6)
   rps2 7 25 1489 15 7 (5) 99.0 78.1 (83.3) 98.6 (98.7) 88.6 (91.2)
   rps3 7 54 2183 19 33 (11) 99.1 62.1 (83.1) 97.7 (98.7) 80.6 (91.1)
   rps4 6 83 1116 22 18 (6) 98.1 82.2 (93.3) 96.8 (97.7) 90.1 (95.7)
   rps7 8 6 664 19 2 (1) 97.2 75.0 (85.7) 97.0 (97.1) 86.1 (91.5)
   rps10 5 8 266 9 0 (0) 96.7 100.0 (100.0) 96.8 (96.8) 98.4 (98.4)
   rps11 3 0 222 1 0 (0) 99.6 - 99.6 (99.6) -
   rps12 17 87 1142 13 5 (1) 98.9 94.6 (98.9) 98.6 (98.9) 96.7 (98.9)
   rps13 10 34 554 8 5 (2) 98.6 87.2 (94.4) 97.8 (98.3) 92.9 (96.5)
   rps14 5 2 239 7 0 (0) 97.2 100.0 (100.0) (97.2) (97.2) 98.6 (98.6)
   rps19 6 16 242 11 9 (3) 95.7 64.0 (84.2) 92.8 (94.9) 79.8 (89.9)
Other
   matR 8 73 4109 30 20 (7) 99.3 78.5 (91.3) 98.8 (99.1) 88.9 (95.3)
   mttB 8 100 1087 41 23 (12) 96.4 81.3 (89.3) 94.9 (95.7) 88.8 (92.8)
Overall 370 3,038 55,956 609 660 (171) 98.9 82.2 (94.7) 97.9 (98.7) 90.5 (96.8)
  1. Values after exclusion of silent editing sites are shown in parentheses. In some cases (marked with a '-'), sensitivity and balanced accuracy could not be calculated because there were no known edited sites (i.e., TP + FN = 0).