Additional file 1 of Identification and validation of a DNA methylation-driven gene-based prognostic model for clear cell renal cell carcinoma

Additional file 1: Supplementary Figure 1. Flow diagram of the analysis procedure, including the discovery, training, and validation stages. Supplementary Figure 2. DMG function. A, GO and C, KEGG functional enrichment analyses of DMGs in the promoter regions of genes. B, GO and D KEGG functional enrichment analyses of DMGs in the gene body regions. Supplementary Figure 3. The expression profile of 18-CpG corresponding genes. Supplementary Figure 4. The DNA methylation profile of promoters of 18-CpG corresponding genes. Supplementary Figure 5. Risk scores in the whole TCGA cohort. A, KM survival curve of patients in the high-risk and low-risk groups. The data are shown as median with the interquartile range. Statistical significance was assessed using Log-rank test. The dotted line shows the statistical significance at 50% survival probability. B, Rank of calculated risk score and survival status of high-risk and low-risk patients. The dotted line shows the cutoff value to distinguish ccRCC high-risk and low-risk patients. C, Heat map of methylation levels at 18 CpG sites. D, The 1-, 3-, 5-, and 10-year ROC curves of risk scores. The sensitivity and specificity of this model were determined by the cutoff value. Supplementary Figure 6. Decision curve analyses for overall survival predictions.The colored lines indicate the net benefit of using the model with the combined clinicopathological characters (red), methylation RiskScore (green) and the NomoScore (black). The assumptions that all patients will be alive and that no patients will be dead are represented by grey and black lines, respectively.

附加文件1：补充图1。分析流程示意图，涵盖发现、训练与验证三个阶段。
补充图2 差异甲基化基因（Differentially Methylated Gene, DMG）功能分析。A、C分别为基因启动子区域差异甲基化基因的基因本体（Gene Ontology, GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）功能富集分析；B、D分别为基因体区域差异甲基化基因的基因本体与京都基因与基因组百科全书功能富集分析。
补充图3：18个CpG位点对应基因的表达谱。
补充图4：18个CpG位点对应基因的启动子区域DNA甲基化谱。
补充图5：全部癌症基因组图谱（The Cancer Genome Atlas, TCGA）队列中的风险评分情况。A：高、低风险组患者的KM生存曲线，数据以中位数及四分位间距展示，统计学显著性采用Log-rank检验进行评估，虚线代表50%生存概率处的统计学显著性阈值。B：高、低风险患者的计算风险评分排序与生存状态分布，虚线为区分肾透明细胞癌（clear cell renal cell carcinoma, ccRCC）高、低风险组的临界值。C：18个CpG位点的甲基化水平热图。D：风险评分的1、3、5、10年受试者工作特征（Receiver Operating Characteristic, ROC）曲线，该模型的灵敏度与特异度由该临界值确定。
补充图6：总生存期预测的决策曲线分析。彩色线条分别代表联合临床病理特征模型（红色）、甲基化风险评分模型（绿色）以及诺模图评分（Nomogram Score, NomoScore）模型（黑色）的净获益。假设所有患者均存活、无患者死亡的情况分别由灰色线条与黑色线条代表。