File S1 - Tumor-Specific Hypermethylation of Epigenetic Biomarkers, Including SFRP1, Predicts for Poorer Survival in Patients from the TCGA Kidney Renal Clear Cell Carcinoma (KIRC) Project

Includes Figures S1-S8 and Tables S1-S9. Figure S1: Gene Map of the CpG Island for the BNC1 gene demonstrating the Positioning of Probes and the Levels of Hypermethylation. Figure S2: The hypermethylated genes present in either both cohorts or just the HumanMethylation27 or 450 BeadChip cohort only. Figure S3: TCGA KIRC hypermethylated genes that occur in regions of common whole/partial chromosomal or focal loss/deletion. Figure S4: Somatic mutation maps for hypermethylated genes in the TCGA KIRC tumors. Figure S5: Kaplan-Meier survival curves for the most hypermethylated probes for each gene from the HumanMethylation450 BeadChip cohort. Figure S6: Relative tumor mRNA expression of selected candidate genes in methylated vs unmethylated tumors in the HumanMethylation450 BeadChip cohort. Figure S7: The WNT pathway and the potentially hypermethylated antagonists. Figure S8: Somatic mutation of the WNT pathway regulating genes and its affect on patient survival. Table S1: The 77 Candidate Hypermethylated Genes for Clear Cell Renal Cell Carcinoma Selected from Published Literature. Table S2: The Methylation Status of the 287 Infinium Probes Representing All 77 Candidate Hypermethylated Genes from the HumanMethylation27 BeadChip Cohort. Table S3: The 182 Hypermethylated Probes from the HumanMethylation450 BeadChip Cohort. Table S4: The Number of Hypermethylated Probes out of all the CpG Island Probes for Each Hypermethylated Gene from the HumanMethylation450 BeadChip Cohort. Table S5: Clinical Information for the HumanMethylation27 BeadChip Cohort and Hypermethylation Status for Significant Genes. Table S6: Clinical Information for the HumanMethylation450 BeadChip Cohort and Hypermethylation Status for Significant Genes. Table S7: Cox Proportional-Hazard Regression Analysis for the Probes that were Statistically Significantly Associated with Poorer Survival in Patients from the HumanMethylation27 BeadChip Cohort compared with Tumor Stage, Tumor Grade, Tumor Maximum Dimension and Patient Gender. Table S8: Kaplan-Meier Survival Curve Analysis for the Single Most Frequently Hypermethylated Probe for each Hypermethylated Gene in the HumanMethylation450 BeadChip Cohort and the Non-Significant Gene Level Results for the HumanMethylation450 BeadChip Cohort. Table S9: Cox Proportional-Hazard Regression Analysis for the Probes or Genes that were Statistically Significantly Associated with Poorer Survival in Patients from the HumanMethylation450 BeadChip Cohort compared with Tumor Stage, Tumor Grade, Tumor Maximum Dimension and Patient Gender. (DOCX)