Figure 5
Analysis of gene expression data from the samples tested for DNA methylation changes. In (a) we again use K-means clustering to identify subsets of genes with distinctive progression of expression patterns during disease progression. Groups III and IV represent genes increasing their expression while groups V and VI show a decrease in expression levels. The significantly differentially expressed genes in a comparison of malignant and control samples (b) are mostly accounted for by genes in groups IV and VI. We associated a candidate enhancer (H3K4me1 positive, H3K4me3 negative) to a gene if the chromatin state was within 5 kb of the gene's transcription start site and showed increased DNA methylation in control versus malignant samples, finding a total of 622 genes fitting these criteria. When we tested to see whether these 622 include genes with significantly altered levels of expression, we showed that these genes with increased DNA methylation were significantly enriched for overlap with genes with decreased expression (P=0.002) but not increased expression (c). In (d) we show the results of analysis of matched HCC and infected liver samples from HCV+ individuals, using data from The Cancer Genome Atlas (TCGA). We tested DNA methylation data from TCGA at candidate enhancers where we had identified increased DNA methylation and found the studies from TCGA to reveal a significant increase of DNA methylation in their samples also. We also compared the genes where we had found significant changes in levels of expression, showing the genes with decreased expression also to have significantly lower levels in TCGA samples, but no significant changes in the levels of expression of genes that we had found to be upregulated with disease progression.
