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Fig. 4 | BMC Genomics

Fig. 4

From: Genome-wide effects of social status on DNA methylation in the brain of a cichlid fish, Astatotilapia burtoni

Fig. 4

Relationships between DNA methylation and gene expression in DMR genes. a: Mean gene expression levels (TPM: transcripts per million, y-axis) across all fish for each DMR gene (dots), plotted as a function of the mean methylation level across all fish (x-axis) for each gene’s DMR(s). b: Heatmap representing Spearman correlations between methylation and gene expression as a function of DMR location (rows). Each row corresponds to a subset of genes with the same color in a-c. Column 1 shows correlations between baseline (mean) gene expression (TPM) and DMR methylation levels (all.mean from Additional file 1: Figure S2 and Additional file 2: Table S1), corresponding to subsets of genes from a. Column 2 shows correlations between expression and DMR fold-differences (see Fig. 2d and Additional file 2: Table S1), corresponding to subsets of genes from d. Darker red and blue colors in cells denote stronger positive and negative correlations, respectively, as shown in legend to right of the heatmap. Spearman’s rho values are shown in cells with p-values < 0.03. c: Boxplot comparing mean gene expression levels across all fish (y-axis) for DMR genes, based on whether DMRs were in the body and/or 5′ or 3′ regulatory regions (x-axis). Omnibus p-value from a Kruskal-Wallis test is reported above the plot, and group sizes are reported in parentheses after the group name under each box. Top and bottom of boxes represent the first and third quartiles, respectively, whiskers extend to the most extreme data points no more than 1.5 times the interquartile range from the box. Dots show data points beyond this range, and horizontal grey line denotes the overall median. *p < 0.05 from Dunn’s post-hoc test with BH-correction. c: Scatterplot of gene expression fold-difference, defined as log2 of D/ND (y-axis), as a function of methylation fold-difference (x-axis) for DMR genes (dots). The same genes are represented in all panels (n = 712). Genes with a DMR in both the 5′ and 3′ regulatory regions are not shown (n = 4). In a, c, d, methylation levels were averaged across all DMRs for genes with > 1 DMR in their body and/or regulatory region(s) (n = 58). In a and d, dashed lines represent the best-fit linear regression, Spearman’s rho is reported above the plot, and gene colors match the color of their corresponding group in c

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