Fig. 7
Combined comparison of DNA methylation, histone modifications and gene expression. a Violin plot of gene expression separated by presence/absence of DNA methylation and histone modifications: H3K4me3 and H3K27me3. The average gene expression in all samples, Fragments Per Kilobase of transcript per Million (FPKM) is log2 scaled. b Venn diagram of genes with DNA methylation and histone modifications, for all genes with detectable modifications above the filtering cutoffs specified in the methods. c Venn diagram for genes, with significant differences (FDR < 0.05) between male and female Daphnia pulex for the modifications. d Heatmap of ranked values for gene expression (FPKM), histone modifications (H3K4me3 and H3K27me3), and DNA methylation (CpG). Red indicates high level of expression or modification, blue indicates low level of expression or modifications. Genes separate into 5 main clusters by omics profile. e Enrichment results for the most significant Reactome pathways in the main clusters from the heatmap (1–5)