Methylated RNA Immunoprecipitation Sequencing Reveals the m⁶A Landscape in Oral Squamous Cell Carcinoma

Figure 7

Pathway enrichment analysis. (a) The pathway enrichment analysis was performed to find metabolic pathways that were significantly enriched in peak-neighboring genes based on the KEGG database, thereby investigating metabolic pathways that might be orchestrated by transcription factors and that might be mediated by transcription factors at different developmental stages and cell states. The pathway enrichment analysis can directly reflect the effect of genes on phenotypes and maximize the relationship between significantly enriched metabolic pathways and phenotypes. The selected peak-neighboring genes were annotated based on the KEGG database to obtain all of the metabolic pathways in which peak-neighboring genes were involved. All of the peak-neighboring genes were assigned to different metabolic pathways. Fisher’s exact test was used to calculate the significance of gene enrichment in each pathway. In order to screen out the metabolic pathways that were significantly enriched in peak-neighboring genes, the top 15 entries were chosen in the pathway enrich analysis where peak-neighboring genes were significantly enriched as the horizontal axis histogram. The horizontal axis in the histogram was employed to show -log10 ( value), and the vertical axis was the pathway name. Meanwhile, the top 25 entries were selected in the pathway enrich analysis in which peak-neighboring genes were significantly enriched as a vertical axis histogram. In the histogram, the horizontal axis showed the pathway name, and the vertical axis represented enrichment. In all charts, red represented significant items, and blue marked nonsignificant items. (b) The results of the pathway enrichment analysis of peak-neighboring genes were presented in a bubble chart. The top 20 pathway entries were selected, in which peak-neighboring genes were significantly enriched for displaying. The ordinate in the figure stood for the pathway entry, and the abscissa indicated the rich factor. The size of the dot in the figure indicated the number of peak-neighbor genes enriched on the pathway entry, and the color represented the significance value of the pathway entry. The smaller the value, the more significant the set. The pathway enrichment degree was measured using the rich factor, value, and the number of genes enriched in this pathway entry. Among them, the rich factor referred to the ratio of the number of peak-neighbor genes enriched in the pathway entry to the number of all genes annotated to the pathway entry. The greater the rich factor, the greater the degree of enrichment.

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