Fig. 5

Hierarchical clustering of the samples from the cellular model of melanoma progression based on the expression of histone-modifying genes in the brown, turquoise, blue, and yellow modules. Genes involved in histone modification (GO term 00165700) were searched among those present in each module. One hundred twenty-six (126) genes associated with histone modification were found in the co-expression modules. The brown module was significantly enriched with these genes (n = 24 genes) and the turquoise, blue, and yellow modules also displayed a high number of histone modification genes, with fourteen, twenty, and fourteen genes, respectively. The Pearson correlation and the complete method were used as the distance metric and linkage method, respectively. Data is represented as z scores, calculated by subtracting the mean and dividing by the standard deviation of the row. The legend shows the color mapping of the row-wise z scores with blue and red colors. The epithelial (melan-a and 4C11+) and mesenchymal (4C and 4C11−) cell lines showed a trend to cluster together based on the expression of genes encoding histone-modifying proteins. a Hierarchical clustering of the samples and histone modification genes from the brown and turquoise modules, showing the most frequent downregulation of these genes in the metastasis-prone 4C11+ cell line. b Hierarchical clustering of the samples and histone modification genes from the blue and yellow modules, showing that these genes were most often upregulated in the samples from the 4C11+ cell line. The module assignment of each gene is shown on the left of the figures by their representative colors.