Additional file 1 of Genome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers

Additional file 1. Table S1: Literature of genome wide DNA methylation analysis in OSCC. Table-S2: Detailed demographic and clinicopathological characteristics of the leukoplakia samples. Table S3: Detailed demographic clinicopathological and characteristics of the OSCC samples. Table S4: Summary of genomewide differentially methylated regions. Table S5: Top 20 differentially methylated CpG sites identified across the leukoplakia samples. Table S6: Top 20 differentially methylated CpG sites identified across the OSCC samples. Table S7: Top 20 differentially methylated CpG islands identified across the leukoplakia samples. Table S8: Top 20 differentially methylated CpG islands identified across the OSCC samples. Table S9: Top 20 differentially hypermethylated and hypomethylated promoters identified across the leukoplakia samples. Table S10: Top 20 differentially hypermethylated and hypomethylated promoters identified across the OSCC samples. Table S11: Top 20 differentially hypermethylated and hypomethylated genes identified across the leukoplakia samples. Table S12: Top 20 differentially hypermethylated and hypomethylated genes identified across the OSCC samples. Table S13: Gene enrichment analysis of top 100 differentially methylated promoters in leukoplakia based on combined rank. Table S14: Gene enrichment analysis of top 100 differentially methylated promoters in OSCC based on combined rank. Table S15: List of differentially methylated promoters common between leukoplakia and OSCC. Table S16: Candidate target gene list obtained from integrative analysis of copy number, gene expression, and DNA methylation data using CNAmet. Table S17: Comparison of our data with TCGA_HNSC cohort. Table S18: Details for pyrosequencing primers. Table S19: Copy number alteration distribution among candidate genes. Table S20: Association between biomarkers and clinicopathological parameters. Table S21: Correlation among different targets. Table S22: Univariate Cox analysis of the association between markers and clinical outcome. Table S23: Univariate Cox analysis of the association between markers and clinical outcome in N0 and N+ group. Table S24: Univariate Cox analysis of the association between markers and clinical outcome in early-stage and advanced-stage groups. Table S25: Prognostic significance of biomarkers based on nodal status and stage of the disease. Table S26: Summary of genomewide differentially methylated regions as a function of deltathreshold. Table S27: Details for TaqMan qPCR CNV assays.附加文件1。附表S1：口腔鳞状细胞癌（OSCC）全基因组DNA甲基化分析相关文献。附表S2：口腔白斑（oral leukoplakia）样本的详细人口统计学与临床病理特征。附表S3：口腔鳞状细胞癌样本的详细人口统计学、临床病理特征。附表S4：全基因组差异甲基化区域汇总。附表S5：口腔白斑样本中筛选得到的前20个差异甲基化CpG位点（CpG sites）。附表S6：口腔鳞状细胞癌样本中筛选得到的前20个差异甲基化CpG位点。附表S7：口腔白斑样本中筛选得到的前20个差异甲基化CpG岛（CpG islands）。附表S8：口腔鳞状细胞癌样本中筛选得到的前20个差异甲基化CpG岛。附表S9：口腔白斑样本中筛选得到的前20个差异高甲基化与低甲基化启动子（promoters）。附表S10：口腔鳞状细胞癌样本中筛选得到的前20个差异高甲基化与低甲基化启动子。附表S11：口腔白斑样本中筛选得到的前20个差异高甲基化与低甲基化基因。附表S12：口腔鳞状细胞癌样本中筛选得到的前20个差异高甲基化与低甲基化基因。附表S13：基于综合排名的口腔白斑前100个差异甲基化启动子的基因富集分析（gene enrichment analysis）结果。附表S14：基于综合排名的口腔鳞状细胞癌前100个差异甲基化启动子的基因富集分析结果。附表S15：口腔白斑与口腔鳞状细胞癌共有的差异甲基化启动子列表。附表S16：通过CNAmet工具整合拷贝数、基因表达与DNA甲基化数据得到的候选靶基因列表。附表S17：本研究数据与TCGA头颈鳞状细胞癌（TCGA_HNSC）队列的对比分析结果。附表S18：焦磷酸测序（pyrosequencing）引物详情。附表S19：候选基因的拷贝数变异（CNV, Copy Number Variation）分布情况。附表S20：生物标志物与临床病理参数的关联分析结果。附表S21：不同靶标间的相关性分析结果。附表S22：标志物与临床结局关联的单变量Cox分析（Cox analysis）结果。附表S23：N0与N+亚组中标志物与临床结局关联的单变量Cox分析结果。附表S24：早期与晚期疾病亚组中标志物与临床结局关联的单变量Cox分析结果。附表S25：基于淋巴结状态与疾病分期的生物标志物预后价值分析结果。附表S26：以δ阈值（deltathreshold）为变量的全基因组差异甲基化区域汇总。附表S27：TaqMan定量聚合酶链反应（TaqMan qPCR）拷贝数变异检测引物详情。