Abnormal Expressions of DNA Glycosylase Genes NEIL1, NEIL2, and NEIL3 Are Associated with Somatic Mutation Loads in Human Cancer
Table 2
Epigenetic silencing of NEIL1 expression in human cancer.
Organ (TCGA ID)
cg number (CpG site ID)
DNA methylation level
Gene expression level
DNA methylation level and gene expression level
Number of cases (N/T)
Difference in the value between the 90th percentile of value in tumor tissue and the mean in normal tissue
Percentage of the hypermethylated tumors
Number of cases (N/T)
Fold expression change between the mean in normal tissue and the mean of the 10% of tumor tissue with the highest value
Number of cases (N/T)
Spearman rank correlation value between DNA methylation and gene expression
Rho
Breast (BRCA)
12978308
96/745
0.109
7.2%
69/723
2.039
69/723
<0.0001
Colon (COAD)
12978308
38/301
0.291
29.9%
19/250
2.087
19/250
<0.0001
Head and neck (HNSC)
12978308
50/529
0.323
57.7%
20/498
2.354
20/498
<0.0001
Kidney (KIRC)
00836571
160/325
0.110
7.1%
24/303
2.407
24/303
<0.0001
Kidney (KIRP)
12978308
45/226
0.351
21.2%
23/182
2.276
23/182
<0.0001
Lung (LUAD)
12978308
32/465
0.109
64.3%
21/422
2.249
21/422
<0.0001
Lung (LUSC)
12978308
42/359
0.254
27.0%
8/358
1.624
8/358
<0.0001
Rectum (READ)
12978308
7/99
0.145
11.1%
2/90
1.998
2/90
0.0003
Stomach (STAD)
12978308
2/325
0.290
40.3%
0/231
2.208
0/231
<0.0001
Epigenetic silencing of the NEIL1 gene was determined according to the following four criteria: () a mean value in normal tissue < 0.4; () a difference in the value between the 90th percentile of value in tumor tissue and the mean in normal tissue > 0.1; () a fold expression change between the mean in normal tissue and the mean of the 10% of tumor tissue with the highest value > 1.5; () a Spearman rank correlation value between DNA methylation and gene expression < −0.25. This table includes only the cancers that fulfilled these four criteria. Percentage of cancers with the following value: the mean value in normal tissue + more than 0.15. Since there is no normal tissue with DNA methylation data in STAD, the mean expression value of 33 gastric normal tissues used in Supplementary Table S2 was utilized for the calculation.
