Legend for Supplementary Files from Identification of DNA Methylation–Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma

Legend and description of Supplementary Figures 1-8</p

Supplementary Figures 1-8, Supplementary Tables 1-3 from Identification of DNA Methylation–Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma

Supplementary Figure 1. Quantitation and location of epigenetic changes in all 6 patient samples. Supplementary Figure 2. Significant accessibility changes between 6 patients. Supplementary Figure 3. Accessibility changes shared in at least two patient samples, plotted in heatmaps, either losing accessibility (Groups a and e) or gaining accessibility (Groups d and f) with or without DNA methylation. Supplementary Figure 4. ChIP-seq analyses of Patient 5. Supplementary Figure 5. Validation of AcceSssIble data from each Group a, d, e, and f using locus-specific bisulfite sequencing. Supplementary Figure 6. Correlation plots of chromatin accessibility and DNA methylation changes vs. gene expression changes. Supplementary Figure 7. Epigenetically-regulated genes in the HIF1A-signaling pathway and VHL status in each ccRCC patient. Supplementary Figure 8. Example diagram of M.SssI treatment efficacy. Supplementary Table 1. List of loci with methylation-dependent accessibility changes that positively correlate with expression changes from TCGA RNA-seq data. Supplementary Table 2. List of loci with methylation-independent accessibility changes that positively correlate with expression changes from TCGA RNA-seq data. Supplementary Table 3. List of genes overlapping between epigenetically-regulated genes from our study, and commonly mutated genes in ccRCC from TCGA.</p

Additional file 1: Figure S1. of Identifying aggressive prostate cancer foci using a DNA methylation classifier

Sample purity. Figure S2. Sample dissimilarity. Figure S3. Unsupervised clustering and heatmaps. Figure S4. Input probes for GLMnet analysis. Figure S5. Distribution of clinical information for the 312 TCGA tumor samples predicted by our classifier. Figure S6. Beeswarm plots. Figure S7. Clinical follow-up information for predicted TCGA tumor samples. Figure S8. Density graph of T-PL dist 2. Table S1. Patient information. LN lymph node. Table S2. PC foci aggressiveness by patient. Table S3. 25-probe aggressiveness classifier. (PDF 1585 kb