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Table 2 CpG dinucleotides examined by methylation-specific polymerase chain reaction

From: The 5'-end transitional CpGs between the CpG islands and retroelements are hypomethylated in association with loss of heterozygosity in gastric cancers

      Primer position* Intensity ratio†
Gene Chromosome locus CpG sites (kb)* CpG ratio GC% U M U U/M‡ M
CDH1 16q22 0 0.73 70 -78 -76 0.92 0.49/0.51 0.94
RABGEF1 7q11 -0.2 1.00 67 -285 -283 0.9 0.46/0.54 0.91
STAG1 3q22 -0.4 0.95 62 -493 -490 0.93 0.51/0.49 0.91
MYBPC2 19q13 -1.2 0.61 61 -1,226 -1,224 0.92 0.48/0.52 0.94
   -0.6 0.83 67 -742 -742 0.9 0.51/0.49 0.88
VDR 12q13 -0.7 0.71 58 -728 -727 0.92 0.51/0.49 0.92
   +0.1 0.84 63 +45 +45 0.95 0.51/0.49 0.94
ESR2 14q23 -0.9 0.66 59 -983 -986 0.85 0.48/0.52 0.91
MLH1 3p22 -1.0 0.43 49 -1,098 -1,098 0.93 0.51/0.49 0.95
   -0.6 0.85 63 -660 -655 0.94 0.48/0.52 0.93
FLJ43855 16p11 -1.1 0.62 55 -1147 -1147 0.89 0.48/0.52 0.90
PTEN 10q23 -1.4 0.66 62 -1,425 -1,425 0.93 0.52/0.48 0.91
   -0.9 0.86 62 -953 -953 0.94 0.51/0.49 0.93
CDKN2A 9p21 -1.5 0.77 65 -1,580 -1,575 0.9 0.47/0.53 0.93
   0 1.10 65 -85 -85 0.91 0.47/0.53 0.91
   +0.8 0.48 51 776 775 0.93 0.51/0.49 0.96
PAX5 9p13 -1.0 0.50 63 -1,056 -1,054 0.92 0.52/0.48 0.90
RUNX2 6p21 -3.8 0.25 36 -3,883 -3,883 0.9 0.48/0.52 0.93
   -3.0 0.71 55 -3,061 -3,061 0.91 0.49/0.51 0.92
   -0.7 0.81 62 -852 -850 0.93 0.52/0.48 0.92
   +1.6 0.63 53 1573 1573 0.92 0.47/0.53 0.94
RUNX3 1p36 -1.7 0.82 60 -1,790 -1,790 0.89 0.46/0.54 0.9
   -0.5 0.94 75 -559 -559 0.91 0.48/0.52 0.9
   -0.1 1.07 76 -219 -217 0.92 0.5/0.5 0.93
   +1.0 0.79 59 952 952 0.91 0.49/0.51 0.93
KIAA1752 16q12 +0.4 0.42 41 391 391 0.92 0.48/0.52 0.94
MUC8 12q24 +2.0 0.42 59 1,909 1,909 0.94 0.49/0.51 0.95
MAGEA2 Xq28 0 0.56 64 -81 -75 0.9 0.54/0.46 0.91
DDX53 Xq22.11 0 0.53 59 -71 -102 0.94 0.48/0.52 0.94
TFF2 21q22 -0.2 0.32 57 -251 -251 0.96 0.5/0.5 0.96
SERPINB5 18q21 -0.3 0.62 51 -315 -308 0.93 0.51/0.49 0.94
MSLN 16q13 -0.8 0.52 57 -827 -827 0.92 0.47/0.53 0.93
  1. *The genomic position was calculated from the May 2004 human reference sequence.
  2. †The relative proportion of unmethylation (U) and methylation (M) band intensity against the total band intensity.
  3. ‡U/M indicates a PCR mixture containing the same amount of the universal methylated and unmethylated DNA.