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Table 4 Integrative analyses for DNA methylation, mRNA expression and CNVs in HCC tumor tissues

From: Integrative epigenomic and genomic filtering for methylation markers in hepatocellular carcinomas

Variables

GRASP

TSPYL5

DNA hypermethylation, No (%)

65 (98.5)

64 (97.0)

mRNA under-expression, No (%)

45 (69.2)

47 (73.4)

 Expression difference, Mean (SD)

−1.63 (1.44)*

−1.67 (1.51)**

 Methylation difference, Mean (SD)

0.55 (0.13)*

0.36 (0.11)**

  Copy number loss, No (%)

4 (8.9)†

1 (2.1)†

  Copy number gain, No (%)

14 (31.1)

33 (70.2)

mRNA over-expression, No (%)

20 (30.8)

17 (26.6)

 Expression difference, Mean (SD)

0.93 (0.79)#

1.12 (1.38)¶

 Methylation difference, Mean (SD)

0.44 (0.30)#

0.39 (0.07)¶

  Copy number gain, No (%)

7 (35.0)‡

12 (70.6)‡

  Copy number loss, No (%)

4 (30.0)

0 (0.0)

  1. * Correlation coefficient = −0.394, p = 0.007; ** Correlation coefficient = −0.415, p = 0.004; †p = 0.153; # Correlation coefficient = −0.199, p = 0.387; ¶ Correlation coefficient = −0.032, p = 0.906; ‡p = 0.031