Figure 6: X-tile plots of the genes that correspond to the five CpGs and network analyses.

X-tile plots of the CpG methylation (993 patients in the entire cohort) and mRNA expression of the five genes (507 patients in the TCGA data set): (a) PITX1, (b) FOXE3, (c) TWF2, (d) EHBP1L1 and (e) RIN1. X-tile plots provide a single and intuitive method to assess the association between marker expression and survival, and automatically select the optimum cut point according to the highest χ²-value defined by Kaplan–Meier survival analysis and log-rank test. Colouration of the plot represents the strength of the association at each division, ranging from low (dark, black) to high (bright, red or green). Red represents inverse association between marker expression and survival, whereas green represents direct association between marker expression and survival. Each pixel represents an individual cutpoint where the number of patients in the group increases as progressed down for the high-expression group (‘larger high population’) or to the right for the low-expression group (‘larger low population’). The dark dots (indicated by arrow) in the X-tile plots are the sites according to the highest χ²-value and are used as the cutoff points separating patients into high-risk and low-risk groups. (f) Network analyses of the genes that correspond to the five CpGs by cBioPortal. PITX1, TWF2 and RIN1 were predicted to have an impact on a diverse network of genes and pathways, as per the cBioPortal for Cancer Genomics network analysis tool. Black line means interactions between the two entities; blue arrow represents that the first entity controls a reaction that changes the state of the second entity. HR, hazard ratio.