Figure 3

Prognostic methylation signatures identified by the “nearest shrunken centroid” algorithm in stage IIIC CM patients. Pre-processed genome-wide methylation data from stage IIIC CM patients under study was analyzed through nearest shrunken centroids algorithm to identify genes best characterizing the k-means defined prognostic methylation groups. Panel a, Shrunken differences for the 17 methylation markers, having at least 1 non-zero difference, selected as signature for LM (blue) and HM (red) groups. Lines to the left indicate relatively reduced levels of methylation; lines to the right indicate relatively increased levels of methylation. Genes defining the signature have been reported as Gene Symbol on the left of the panel. Duplicate Gene Symbol entries refer to methylation data read for the same gene from different probes. Panel b, the methylation values of the 17 genes composing the methylation signature in the patients’ population have been reported as a heatmap. Genes defining the signature have been reported as Gene Symbol on the right of the heatmap, while patient identifier numbers and the k-means-defined groups have been reported on foot of the heatmap. Duplicate Gene Symbol entries refer to methylation data read for the same gene from different probes. Each color patch represents the methylation level of one gene in each patient, with a continuum of methylation levels from dark blue (completely unmethylated, β = 0) to dark red (completely methylated, β = 1).