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Table 2 TP53 signaling pathway genes showing inverse relation between promoter DNA methylation and mRNA expression

From: Gene promoter and exon DNA methylation changes in colon cancer development – mRNA expression and tumor mutation alterations

Gene symbol Gene name promoter DNA methylation in our Metcap-Seq study* mRNA expression in tumor/adenoma versus normal
(logFCmin and logFCmax)**
Alterations in cancer/CRC/adenoma***
BAX BCL2 associated X, apoptosis regulator hypomethylated in adenoma 0.36 and 1.09 - downregulation in CRC [72]
CDK1 cyclin dependent kinase 1 hypomethylated in adenoma 0.42 and 2.12 - overexpression in cancer [73]
CDKN1A (p21) cyclin dependent kinase inhibitor 1A hypermethylated in CRC −2.16 and − 0.67 - loss of expression in CRC [74]
CDKN2A (p16) cyclin dependent kinase inhibitor 2A hypermethylated in CRC
hypermethylated in adenoma
−0.81 - hypermethylated in CRC [75, 76] and in adenoma [76]
CYCS cytochrome c, somatic hypermethylated in CRC
hypermethylated in adenoma
−0.43 and − 1.83;
− 0.33 and − 1.27
- loss of protein expression in CRC and in adenoma [77]
- its downregulation correlates with apoptosis resistance [77]
DDB2 damage specific DNA binding protein 2 hypomethylated in adenoma 1.31 and 1.54 - suppresses tumorigenicity [78]
- reduces invasiveness of CRC [79]
- downregulated in high-grade CRC [79]
GTSE1 G2 and S phase expressed hypomethylated in CRC
hypomethylated in adenoma
0.27 and 2.61 - upregulation in several tumor types [80, 81]
IGFBP3 insulin like growth factor binding protein 3 hypermethylated in CRC
hypermethylated in adenoma
−1.11 and − 2.27 - hypermethylated in lung cancer [82]
- downregulation in esophageal carcinoma [83]
- lower level is associated with increased colon adenoma risk [84]
SESN2 sestrin 2 hypermethylated in CRC −1.86 and − 0.72 - downregulation in tumors [85,86,87]
- predicts unfavorable CRC outcome [85]
SESN3 sestrin 3 hypomethylated in CRC 0.46 and 1.09 - involved in in vitro resistance to Irinotecan [88]
  1. *Δβ-values see in Table 1
  2. **according to Affymetrix HGU133Plus2.0 microarray data (GEO accession numbers: GSE37364 [28], GSE18105 [29], GSE4107 [30], GSE9348 [31], GSE22242 [32], GSE8671 [33])
  3. ***according to previous literature data