Table 2.
CpG dinucleotides examined by methylation-specific polymerase chain reaction
| 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 |
*The genomic position was calculated from the May 2004 human reference sequence.
†The relative proportion of unmethylation (U) and methylation (M) band intensity against the total band intensity.
‡U/M indicates a PCR mixture containing the same amount of the universal methylated and unmethylated DNA.