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Table 5 Methylation alterations in the CpG islands and the 5'-transitional CpG sites examined in gastric cancers containing high-level and low-level chromosomal losses

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

  High-level chromosomal loss (n = 20) Low-level chromosomal loss (n = 19)
  Mean level of methylation   Methylation alterations (%) Mean level of methylation   Methylation alterations (%)
CpG sites* Normal Tumor p† Hypo- Hyper- Normal Tumor p† Hypo- Hyper-
CpG islands           
   CDH1, 0 kb 1.2 1.0 0.083 3 (15) 0 (0) 1.1 1.1 0.560 0 (0) 1 (5)
   RABGEF1, -0.2 kb 1.1 1.0 0.163 2 (10) 0 (0) 1.0 1.0 1 0 (0) 0 (0)
   STAG1, -0.4 kb 1.1 1.0 0.330 1 (5) 0 (0) 1.0 1.0 1 0 (0) 0 (0)
   MYBPC2, -0.6 kb 1.6 1.6 0.757 2 (10) 1 (5) 2.0 2.3 0.090 0 (0) 4 (21)
   MLH1, -0.6 kb 1.4 1.4 1 5 (25) 2 (10) 1.3 1.7 0.153 0 (0) 4 (21)
   PTEN, -0.9 kb 1.3 1.2 0.442 2 (10) 0 (0) 1.1 1.1 0.560 1 (5) 2 (11)
   CDKN2A, 0kb 1.1 1.0 0.330 1 (5) 0 (0) 1.0 1.4 0.072 0 (0) 4 (21)
   PAX5, -1.0 kb 2.0 1.7 0.115 7 (35) 0 (0) 1.9 2.1 0.505 4 (21) 5 (26)
   RUNX2, -3.8 kb 4.2 3.8 0.054 7 (35) 0 (0) 4.2 4.3 0.376 1 (5) 4 (21)
-3.0 kb 1.8 1.8 1 5 (25) 5 (25) 2.0 2.0 1 3 (16) 4 (21)
-0.7 kb 2.1 2.0 0.575 5 (25) 4 (20) 1.7 1.9 0.266 4 (21) 6 (32)
+1.6 kb 2.0 2.2 0.295 3 (15) 5 (25) 2.1 2.5 0.066 2 (11) 7 (37)
   RUNX3, -1.7 kb 2.0 3.3 <0.0001 0 (0) 14 (70) 2.5 3.3 0.012 0 (0) 12 (63)
-0.5 kb 1.3 1.1 0.121 6 (30) 2 (10) 1.8 2.4 0.035 2 (11) 9 (47)
-0.1 kb 1.2 1.0 0.042 4 (20) 0 (0) 1.0 1.2 0.042 0 (0) 4 (21)
+1.0 kb 4.0 3.8 0.519 6 (30) 5 (25) 3.4 3.8 0.012 0 (0) 7 (37)
   VDR, +0.1 kb 1.0 1.0 1 0 (0) 0 (0) 1.0 1.0 1 0 (0) 0 (0)
   KIAA1752, +0.4 kb 2.8 2.6 0.096 8 (40) 0 (0) 2.1 2.5 0.084 0 (0) 7 (37)
Transitional CpGs           
   MYBPC2, -1.2 kb 4.3 4.1 0.083 4 (20) 0 (0) 4.3 4.2 0.546 5 (26) 2 (11)
   VDR, -0.7 kb 1.8 1.3 0.003 10 (50) 0 (0) 1.5 2.1 0.056 3 (16) 8 (42)
   ESR2, -0.9 kb 1.7 1.4 0.114 6 (30) 0 (0) 1.3 1.5 0.141 0 (0) 4 (22)
   MLH1, -1.0 kb 3.1 2.5 0.050 9 (45) 2 (10) 2.8 3.5 0.035 1 (5) 11 (58)
   FLJ43855, -1.1 kb 4.0 3.5 0.043 10 (50) 2 (10) 3.7 4.1 0.072 2 (11) 8 (42)
   PTEN, -1.4 kb 1.4 1.1 0.062 5 (25) 0 (0) 1.1 1.3 0.119 1 (5) 5 (26)
   CDKN2A, -1.5 kb 2.0 1.6 0.012 10 (50) 2 (10) 2.0 2.8 0.025 3 (16) 10 (53)
+0.8 kb 4.4 3.6 0.002 12 (60) 0 (0) 4.1 4.4 0.173 3 (16) 7 (37)
   MUC8, +2.0 kb 4.4 3.7 0.001 9 (45) 0 (0) 4.4 4.2 0.149 6 (32) 2 (11)
   MAGEA2, 0 kb 4.8 3.4 <0.0001 11 (55) 0 (0) 4.8 4.6 0.336 2 (11) 0 (0)
   DDX53, 0 kb 4.2 3.7 0.051 9 (45) 2 (10) 4.5 3.9 0.096 6 (32) 2 (11)
   TFF2, -0.2 kb 2.4 2.1 0.174 7 (35) 2 (10) 2.2 2.0 0.324 6 (32) 2 (11)
   SERPINB5, -0.3 kb 2.7 2.2 0.080 10 (50) 3 (15) 2.4 2.5 0.598 2 (11) 4 (21)
   MSLN, -0.8 kb 4.3 3.6 0.005 11 (55) 2 (10) 3.5 3.7 0.591 1 (5) 5 (26)
  1. *CpG sites are indicated by the name of the gene and the distance from the transcription start site.
  2. †p values were calculated by an independent t test for the mean values.