Figure 5

Development and validation of prognostic methylation-related differentially expressed genes (mrDEGPS) model in oral squamous cell carcinoma (OSCC) samples. (A) UpSet plot of number of positively correlated CpGs (PosCpGs) (turquoise), negatively correlated CpGs (NegCpGs) (pink), and DMCpGs (black border) in OSCC samples. The intersections of differentially methylated CpGs (DMCpGs) with PosCpGs or NegCpGs were expressed using turquoise or pink bars with black border. (B) UpSet plot of number of genes with PosCpGs (PosCpG-Gene, turquoise), NegCpGs (NegCpG-Gene, pink), and DEGs (black border) in OSCC samples. The intersections of DEGs with PosCpG-Genes or NegCpG-Genes were expressed using turquoise or pink bars with black border. The intersections between PosCpG-Genes and NegCpG-Genes were expressed using graduating color from turquoise to pink. (C) Partial results of multivariate Cox proportional hazards regression analysis of mrDEGs using the cutoff of P < 0.01. MrDEGs were defined as DEGs with posCpG, NegCpG, or both. The vertical dotted line was the invalid line of HR = 1. The mrDEGs located on the left and right of the invalid line were prognosis-beneficial and prognosis-harmful mrDEGs colored in turquoise and pink, respectively. (D) MrDEGPS and overall survival (OS) in patients sequenced by increasing mrDEGPS. The low- and high-risk patients were divided by the cutoff of mrDEGPS = 1.0256. OS was calculated based on the follow-up time, if patients survived (blue), or time until death (red). (E) Heatmap of high- and low-risk OSCC samples grouped by mrDEGPS according to the simulation result of mrDEGPS model. The heatmap shows mrDEGs arranged in rows (upregulation colored in red and downregulation in dark blue) and samples in columns (high-risk OSCC samples colored in pink and low-risk OSCC samples in turquoise). (F) Kaplan–Meier plots for OS, disease-specific survival, and progression-free survival grouped by low- and high-risk patients in the training set (The Cancer Genome Atlas (TCGA) dataset)). (G) Kaplan–Meier plots for OS grouped by low- and high-risk patients in a validation set (GSE41613). (H) Box plots of mrDEGPS grouped by different clinical features including age, gender, clinical stage, alcohol habit, histopathological grade, HPV infection, lymphovascular invasion, surgical margin, and perineural invasion in the training set (TCGA dataset). *, **, and ***indicate P < 0.05, P < 0.01, and P < 0.001, respectively. (I) Violin plot of mrDEGPS grouped by HPV (+), HPV (−), and HPV status not available (NA) in a validation set (GSE87053).