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Fig. 3 | Clinical Epigenetics

Fig. 3

From: Gene co-expression and histone modification signatures are associated with melanoma progression, epithelial-to-mesenchymal transition, and metastasis

Fig. 3

Co-expression interactions and hazard ratios for genes belonging to modules with prognostic value in the Leeds Melanoma cohort data. Multivariate analyses were performed by adjusting (i) age, sex, and tumor site (MA1 analysis) or (ii) as above plus AJCC stage and mitotic rate (MA2 analysis). Genes from the turquoise module were significantly overrepresented with genes with prognostic value in both MA1 (n = 80 genes, p = 2.4 × 10−12) and MA2 (n = 49 genes, p = 5.1 × 10−10) models. The green yellow module showed a significant overrepresentation of prognostic genes in the MA1 (p = 0.017, n = 10 genes), whereas the midnight blue and salmon modules showed a trend to be enriched with prognostic genes in the MA1 (p = 0.083, n = 7 genes; p = 0.060, n = 8 genes, respectively). a Co-expression network showing the relationships between the 80 genes from the turquoise module that were identified as prognostic genes in the MA1; the borders of the nodes representing genes with the highest (detrimental) and lowest (protective) hazard ratios were colored in red and blue, respectively. b Forest plot showing the hazard ratios (HR) and 95% confidence intervals for the genes from the turquoise module in the MA1; HR between 0 and 1 (protective) or larger than 1 (detrimental) are shown in blue and red colors, respectively. Circles represent the HR and the horizontal lines extend from the lower to the upper limit of the 95% confidence interval for the estimated HR. c Co-expression network showing the interactions between the 49 genes from the turquoise module that were identified as prognostic genes in the MA2. d Forest plot showing the hazard ratios (HR) and 95% confidence intervals for the genes from the turquoise module in the MA2; HR between 0 and 1 (protective) or larger than 1 (detrimental) are shown in blue and red colors, respectively. e Forest plot displaying the hazard ratios (HR) and 95% confidence intervals for the genes from the green yellow, midnight blue, and salmon modules in the MA1 model; the dots and lines were colored according to the module assignment of each gene for visualization purposes

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