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

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

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*	•	•	-

•: 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.