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Table 3 ROC analysis of DNA methylation markers for UC

From: Diagnostic markers of urothelial cancer based on DNA methylation analysis

Gene Cut-off value (%) AUC Sensitivity (%) Specificity (%) P value
Validation in tissue (N/CN vs. T)     
Hypermethylation      
SOX1 32.59 0.97 93.62 97.5 5.13E-14
TJP2 71.42 0.92 84.91 97.78 1.19E-12
MYOD 26.0 0.91 75.0 79.83 1.73E-12
HOXA9_1 55.59 0.86 76.6 97.83 9.00E-08
HOXA9_2 29.06 0.86 83.02 97.83 5.22E-10
Hypomethylation      
VAMP8 12.5 0.96 94.34 97.83 2.22E-15
CASP8 23.18 0.96 94.34 95.65 4.88E-15
SPP1 26.14 0.95 86.79 100 1.49E-14
IFNG 64.7 0.93 82.98 95.65 2.16E-12
CAPG 16.21 0.93 83.02 95.65 1.08E-12
HLADPA1 14.31 0.88 84.62 86.96 1.06E-09
RIPK3 22.97 0.85 81.63 84.44 9.54E-07
Validation in tissue (N vs. CN)
Hypermethylation      
SOX1 16.51 0.86 68.18 100 9.04E-05
MYOD 12.71 0.85 76.0 85.71 5.19E-05
HOXA9_1 22.95 0.80 76.0 80.95 0.00043
GALR1 7.24 0.85 76.0 85.71 4.26E-05
IPF1 33.83 0.74 64.0 76.19 0.0089
TAL1 29.47 0.83 76.0 85.71 0.00011
EYA4 6.38 0.80 83.33 73.68 0.0078
CDH13 7.13 0.93 88.0 85.71 5.24E-07
CYP1B 13.61 0.75 60.0 80.95 0.0040
NPY 10.31 0.82 88.0 71.43 0.00018
Hypometylation      
CASP8 46.38 0.73 60.0 85.71 0.0084
IFNG 84.93 0.78 56.0 95.24 0.001
HLADPA1 24.27 0.83 72.0 85.71 0.00011
Validation in urine sediment (NU vs. TU)    
Hypermethylation      
SOX1 15.62 0.74 41.54 100 0.0041
TJP2 7.933 0.79 92.54 56.25 0.0003
MYOD 9.897 0.93 86.79 87.50 3.10E-05
HOXA9_1 7.038 0.92 86.23 88.89 4.25E-05
HOXA9_2 3.20 0.81 88.57 61.54 0.0004
Hypomethylation      10.78
VAMP8 10.78 0.72 97.06 40.0 0.023
CASP8 7.863 0.82 73.61 76.92 0.0005
SPP1 21.23 0.79 85.94 75.0 0.0015
IFNG 86.08 0.76 55.07 92.31 0.0037
CAPG 8.08 0.67 83.82 56.25 0.04
HLADPA1 6.46 0.82 77.19 90.0 0.0009
RIPK3 9.37 0.75 82.35 70.0 0.011
  1. Selected loci that were identified as either hyper- or hypo-methylated were analyzed for their degree of DNA methylation and association with UC. The loci are named by the genes in which they occur; if there are 2 loci in the same gene, the suffixes 1 and 2 are added.