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Fig. 2 | BMC Medical Genomics

Fig. 2

From: Genes CEP55, FOXD3, FOXF2, GNAO1, GRIA4, and KCNA5 as potential diagnostic biomarkers in colorectal cancer

Fig. 2

Heatmap representing methylation, some clinical and genetic data. RPMM-based classification of 381 of tumor samples from colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ) project in TCGA and heatmap representation of HM450 DNA methylation data. DNA methylation profiles of 4165 probes with most variable DNA methylation values (standard deviation > 0.25) in the 381 colorectal tumor sample set. The DNA methylation β-values are represented by a color scale from blue (low DNA methylation) to red (high DNA methylation). The probes are arranged based on the order of unsupervised hierarchal cluster analysis. Four subgroups were derived by RPMM-based clustering and are indicated below the heatmap: (red) CIMP-H cluster (n = 59); (black) CIMP-L cluster (n = 104); (blue) Cluster 3 (n = 124); (green) Cluster 4 (n = 94). Below methylation cluster is location: (dark green) ascending colon, (light blue) descending colon, (yellow) transverse colon, (purple) sigmoid colon, (orange) rectum, (grey) NA – data not available; gender: (light brown) female, (dark gray) male; tumor stage: (navy blue) stage I, (pink) stage II, (light green) stage III, (turquoise) stage IV, (gray) NA – data not available; MLH1 methylation (gold bars), BRAF mutation (olive bars), KRAS mutation (dark red bars), APC mutation (dark brown bars) and TP53 mutation (violet bars). On the right side of the heatmap are methylation levels of the samples from normal colorectal mucosa (n = 45) for comparison. The average age of patients is 64.2 and the average age of patients with normal mucosa is 68.8. Figure was prepared using library ComplexHeatmap in R programming software

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