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Table 1 Differentially methylated genes as revealed by genome-wide methylation analysis, which were selected for validation by pyrosequencing and RT-qPCR

From: Genome-wide methylation and transcriptome analysis in penile carcinoma: uncovering new molecular markers

Genes MCIp-chip Pyrosequencing Expression (RT-qPCR)
RSPO2 Underexpressed
TWIST1 Underexpressed
SOX3* Underexpressed
SOX17 Underexpressed
PROM1/CD133 Underexpressed
HOXA3* Underexpressed
MEIS1 Underexpressed
OTX2 Underexpressed
SOX14 N.S.
ONECUT1 N.S.
PAX7 N.S.
FOXA1 N.S.
LHX5 -
BDNF -
NKX2.2 -
NKX2.3 -
CDX2 -
ONECUT2 -
LIN28A -
WIT1 -
  1. •: methylated probe, P value ≤0.05; N.S.: not significant; − not performed; *For these genes, P value ≤0.05 was obtained from the Mann–Whitney test. For all other genes, significance was obtained using the Kruskal-Wallis test.