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. 2023 Mar 15;18(11):2489–2496. doi: 10.4103/1673-5374.371399

Figure 4.

Figure 4

Changes of DMRs in CpG, CHG, and CHH contexts after SCI.

(A) Heatmaps of methylation levels of DMRs in CpG, CHG, and CHH at promoters. The raw methylation datasets of genomic elements with all CpG, CHG, and CHH contexts were obtained from the SeqMonk software. Kruskal-Wallis test was performed to analyze the differences among sham and SCI groups. The ComplexHeatmap R package was used to generate the heatmap. The red, black, green, and blue bars indicate the sham, early, intermediate, and late groups, respectively. The numbers of the DMRs are shown on the left; legends for the methylation levels are at the bottom. (B) Gene Ontology analysis of promoter DMRs in CpG context with the clusterProfile R package. Each time group is compared to the sham group with logistics regression in the SeqMonk (P < 0.05, observation > 10). The DMRs were processed with clusterProfiler R package. The P value cutoff was 0.05, q value cutoff was 0.05, P adjust method was BH. Then the cnetplots were generated to show the functional annotation. DMR: Differential methylation region; SCI: spinal cord injury; UTR: untranslated region.