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.