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Table 2 Differentially methylated cytosines (DMCs; q < 0.05) decreased post-surgery versus pre-surgery

From: Weight loss after Roux-En-Y gastric bypass surgery reveals skeletal muscle DNA methylation changes

Chr Position Gene Pre-surgery methylation % Post-surgery methylation % P value q value Genic region CpG region
chr19 9,271,227 ZNF317 99.54 ± 0.46 88.87 ± 2.27 8.86E−09 0.0020 Exon CpG_Island
chrX 41,782,532 CASK 36.44 ± 4.47 7.49 ± 1.49 1.61E−08 0.0028 Promoter CpG_Island
chr9 134,346,329 PRRC2B 99.15 ± 0.57 86.92 ± 2.80 1.69E−08 0.0028 Exon InterCpgi
chr15 101,420,903 ALDH1A3 81.98 ± 2.87 58.77 ± 5.28 3.90E−08 0.0050 Intron CpG_Island
chr3 13,696,951 LOC285375 9.02 ± 2.58 0 ± 0 3.63E−08 0.0050 Intergenic CpG_Island
chr11 70,008,217 ANO1 99.47 ± 0.53 82.21 ± 2.68 6.57E−08 0.0079 Intron InterCpgi
chr5 9,509,512 SEMA5A 100 ± 0 91.29 ± 2.45 8.58E−08 0.0091 utr5 InterCpgi
chr19 48,824,452 ≠  CCDC114 79.96 ± 2.47 52.67 ± 3.92 1.11E−07 0.0105 Promoter North_shore
chr19 48,824,452 ≠  EMP3 79.96 ± 2.47 52.67 ± 3.92 1.11E−07 0.0105 Promoter North_shore
chr15 76,634,525 ISL2 6.79 ± 1.30 0 ± 0 1.09E−07 0.0105 utr3 CpG_Island
chr16 1,774,262 MAPK8IP3 96.07 ± 0.89 86.94 ± 2.61 1.36E−07 0.0116 Intron InterCpgi
chr15 62,457,572 C2CD4B 52.02 ± 4.77 15.90 ± 4.03 1.48E−07 0.0122 Promoter CpG_Island
chr16 89,687,436 DPEP1 74.63 ± 2.21 46.44 ± 4.95 1.80E−07 0.0135 utr5 InterCpgi
chr17 45,330,989 ITGB3 13.64 ± 2.74 0.51 ± 0.51 1.96E−07 0.0135 Promoter CpG_Island
chr9 104,075,142 LPPR1 100 ± 0 82.89 ± 5.22 2.13E−07 0.0135 Exon InterCpgi
chr16 30,990,627 SETD1A 86.89 ± 3.56 57.56 ± 5.29 1.84E−07 0.0135 Exon North_shore
chr12 54,345,965 HOXC12 15.68 ± 1.11 3.11 ± 1.14 2.69E−07 0.0159 Intergenic South_shore
chr19 619,189 POLRMT 99.40 ± 0.6 91.17 ± 1.00 3.34E−07 0.0188 Intron CpG_Island
chr11 628,172 CDHR5 100 ± 0 89.48 ± 2.13 3.74E−07 0.0192 Promoter South_shore
chr11 628,172 SCT 100 ± 0 89.48 ± 2.13 3.74E−07 0.0192 Promoter South_shore
chr10 88,269,670 WAPAL 99.68 ± 0.32 91.58 ± 1.90 3.76E−07 0.0192 Intron InterCpgi
chr1 235,979,239 LYST 42.96 ± 5.36 15.09 ± 3.25 3.94E−07 0.0197 Intron InterCpgi
chr19 50,098,039 PRR12 87.92 ± 1.83 67.43 ± 3.66 4.39E−07 0.0216 Exon CpG_Island
chr8 101,723,031 PABPC1 83.96 ± 3.70 42.12 ± 5.68 4.62E−07 0.0219 Intron InterCpgi
chr15 23,932,055 NDN 39.77 ± 5.54 14.89 ± 3.47 4.81E−07 0.0222 Exon CpG_Island
chr5 1,491,652 LPCAT1 98.22 ± 1.19 79.85 ± 3.10 5.04E−07 0.0226 Intron South_shore
chr11 61,486,429 DAGLA 58.08 ± 3.83 34.62 ± 3.51 5.53E−07 0.0241 utr5 North_shore
chr3 126,746,778 PLXNA1 100 ± 0 87.57 ± 1.95 5.87E−07 0.0251 Intron North_shore
chr15 23,892,609 MAGEL2 54.77 ± 8.17 19.70 ± 3.99 6.66E−07 0.0276 Exon InterCpgi
chr4 111,553,834 PITX2 88.67 ± 3.28 55.56 ± 9.64 7.47E−07 0.0297 Intron CpG_Island
chr17 79,497,291 FSCN2 57.24 ± 5.14 29.65 ± 3.61 8.94E−07 0.0308 Intron South_shore
chr14 24,666,733 TM9SF1 93.83 ± 2.06 71.93 ± 3.85 8.75E−07 0.0308 Promoter South_shore
chr21 43,859,102 UBASH3A 86.97 ± 2.24 68.44 ± 4.45 8.62E−07 0.0308 Intron InterCpgi
chrX 152,600,028 ZNF275 48.08 ± 2.35 25.34 ± 3.90 8.31E−07 0.0308 utr5 CpG_Island
chr4 3,678,810 LOC100133461 93.87 ± 2.40 63.82 ± 6.14 9.43E−07 0.0317 Intergenic InterCpgi
chr13 67,135,465 PCDH9 98.97 ± 0.50 89.39 ± 1.64 1.14E−06 0.0370 Intron InterCpgi
chrX 10,188,915 CLCN4 100 ± 0 91.75 ± 2.13 1.42E−06 0.0419 Exon InterCpgi
chr18 34,274,365 FHOD3 59.66 ± 4.19 34.53 ± 3.20 1.51E−06 0.0429 Intron InterCpgi
chr20 62,329,849 TNFRSF6B 76.74 ± 2.63 57.78 ± 4.65 1.62E−06 0.0448 Exon South_shore
chr15 101,421,027 ALDH1A3 79.81 ± 3.85 54.34 ± 5.33 2.04E−06 0.0479 Intron CpG_Island
chr20 3,778,167 CDC25B 95.43 ± 1.99 75.05 ± 3.37 1.90E−06 0.0479 utr5 South_shore
chr7 27169037^ HOXA3 94.58 ± 1.54 78.97 ± 4.24 1.96E−06 0.0479 Exon North_shore
chr7 27169037^ HOXA4 94.58 ± 1.54 78.97 ± 4.24 1.96E−06 0.0479 Exon north_shore
chr6 100,906,424 SIM1 49.04 ± 2.93 18.82 ± 4.42 2.00E−06 0.0479 Intron CpG_Island
chr22 19,747,159 TBX1 44.30 ± 4.95 22.56 ± 2.96 2.14E−06 0.0498 utr5 South_shore
  1. Data are mean ± SEM. The P value is calculated from the MethylSig analysis. The q value is generated by Benjamini–Hochberg multiple testing correction
  2. Two genes [SCT and CDHR5] are associated with the same differentially methylated cytosine [Chr11:628172]; ≠ Two genes [EMP3 and CCDC114] are associated with the same differentially methylated cytosine [Chr19: 48824452]
  3.  Two genes [EMP3 and CCDC114] are associated with the same differentially methylated cytosine [Chr19: 48824452]
  4. ^Two genes [HOXA3 and HOXA4] are associated with the same differentially methylated cytosine [Chr7: 27169037]