Figure 5
From: Genome-wide methylation analysis identifies genes silenced in non-seminoma cell lines
Graphical representation of selected methylated genes and validation of differential expression. For each gene, panels show (a) graph of average methylation across CpG islands in the four cell lines, (b) level of expression from array analysis (‘Relative expression level (microarray analysis)’ represents the signal relative to control probes), (c) RT–PCR analysis, (d) graph of CpG density across the gene structure (green bar indicates position of the promoter) and (e) level of methylation at each CpG included in 450 K chips relative to CpG features in d. Promoter prediction was achieved using the Eukaryotic Promoter Database (http://epd.vital-it.ch) for identification of transcription start sites (TSSs) together with a review of the literature for each gene; gene sequences were submitted to the MethPrimer programme (http://www.urogene.org/methprimer/) to identify CpG sites and islands. Blue vertical bars represent CpG islands, red vertical bars below graphs represent CpG sites.
