Abnormal Expressions of DNA Glycosylase Genes NEIL1, NEIL2, and NEIL3 Are Associated with Somatic Mutation Loads in Human Cancer
Table 3
Associations between NEIL3 and APOBEC3B expression levels in human cancer.
Organ
TCGA ID
Number of cases
Mann-Whitney test
Spearman rank correlation
Grouped by NEIL3 expression level (<2.5/2.5)
(“increase” or “decrease” in APOBEC3B expression)
Rho
P
Median APOBEC3B expression
Number of cases
Urinary bladder
BLCA
241
146/382
18/223
0.0034 (increase)
0.0697
0.2811
Breast
BRCA
1056
45/175
76/980
<0.0001 (increase)
0.5215
<0.0001
Colon
COAD
260
169/231
108/152
0.0191 (increase)
0.1569
0.0113
Head and neck
HNSC
498
501/466
209/289
0.2122
0.2326
<0.0001
Kidney
KICH
66
132/149
28/38
0.5463
0.1312
0.2935
Kidney
KIRC
519
26.9/65.1
31/488
<0.0001 (increase)
0.5777
<0.0001
Kidney
KIRP
198
33.1/55
22/176
0.0017 (increase)
0.4466
<0.0001
Lung
LUAD
490
60.4/159
43/447
<0.0001 (increase)
0.2759
<0.0001
Lung
LUSC
490
195/496
5/485
0.0187 (increase)
0.1302
0.0039
Prostate
PRAD
333
19/32.9
97/236
<0.0001 (increase)
0.5876
<0.0001
Rectum
READ
92
172/247
36/56
0.0985
0.1559
0.1379
Stomach
STAD
238
2.75/3.92
79/159
0.0007 (increase)
0.1848
0.0042
Thyroid gland
THCA
508
37.2/66.5
276/232
<0.0001 (increase)
0.4242
<0.0001
A value 2.5-fold the median NEIL3 expression value in noncancerous tissue samples of each organ was used as the cut-off value to dichotomize the cancer cases. Higher numbers of median APOBEC3B expression values are shown in bold face. RPKM value was used to show expression level in stomach cancer; on the other hand RSEM value was used in the other organs’ cancers. A Mann-Whitney test was used to perform the statistical analysis. If the value was less than 0.05, indicating a significant change, a significant “increase” or “decrease” in the APOBEC3B expression was shown. If significant (less than 0.05), the value was shown in bold face.
