Figure 3
From: Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy

Differentially expressed genes over three models of TLE.
(a–c) - Unsupervised hierarchical clustering of samples and transcripts according to differential expression profiles (upregulation - red, downregulation - blue, cut-off p < 0.001) for the amygdala stimulation (a), TBI (b) and pilocarpine model (c). Green bars on the top of the heatmaps refer to control and magenta bars to SE/TBI animals. Data from pilocarpine model were previously published by Kobow et al.10 and reanalyzed here as described in Methods section. (d) - Heatmap presenting genes with altered expression levels in at least two animal models (cut-off p < 0.001). Blue color indicates downregulation and red upregulation of gene expression in a given model of epilepsy. The blue bar on the top of the heatmap refers to control and the magenta bar to SE/TBI animals. Black shadings on the left side of the heatmap represent the significant differences. (e–f) - Venn diagrams presenting upregulated (e) or downregulated (f) genes common between models. (g) - Direct and indirect experimentally observed interaction between genes or gene products according to IPA. Note that interactions were found between Msn (moesin) and Cd44 (Cd44 antigen precursor) and that feedback interaction was observed for S100a6, Msn and Cd44. (h) - Word clouds presenting enrichment analysis of terms from the GO database from the Biological Process branch and terms from biological pathways databases (KEGG and Reactome) with gProfiler for each model. The length of blue and red bars over each word cloud are proportional to the number of down- and upregulated genes, respectively. The numbers on the right side of the bars (G1 and G2) represent the number of down- and upregulated genes, respectively. Word clouds under the blue bars describe enriched terms for downregulated genes whereas words under the red bars represent upregulated genes. Only significantly enriched terms (enrichment p < 0.01) are presented. The color of the font indicates the enrichment p-value. Darker colors indicate more significant enrichment. The font size is related to the significance of enrichment of a given term but only within a given cloud.