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

Figure 6

Gene Ontology (GO) enrichment analysis. (a) GO enrichment analysis aimed to obtain significantly enriched GO entries to show gene functions that might be regulated by transcription factors. Each peak-neighboring gene was annotated with GO to harvest all of its GO function entries, and all peak-neighboring genes were assigned to different levels of MF (molecular function), BP (biological process), and CC (cellular component). In the GO functional classification, Fisher’s exact test was adopted to calculate the significance level of gene enrichment in each GO classification to screen out the GO classifications that were significantly enriched in the peak-neighboring genes. The top 15 items of GO items that were significantly enriched in the peak-neighboring genes were selected as a histogram, and the significance threshold was value < 0.05. The horizontal axis histogram was taken as an example to display the GO enrichment analysis of all peak-neighboring genes. On the leftmost was BP, in the middle was MF, and on the rightmost was CC. The horizontal axis of each graph was -log10 ( value), and the vertical axis was the name of the GO items. (b) The results of the GO enrichment analysis of peak-neighboring genes were presented in a bubble chart format, with the top 20 GO entries that were significantly enriched in peak-neighboring genes displayed. In the figure, the ordinate indicated the GO entry, and the abscissa marked the rich factor. The size of the dot in the figure indicated the number of peak-neighboring genes enriched on the GO entry, and the color illustrated the significance value of the GO entry. The smaller the value, the smaller the enrichment and the more significant the set. The degree of the GO enrichment was measured using the rich factor, value, and the number of genes enriched in this GO entry. Among them, the rich factor referred to the ratio of the number of peak-neighboring genes enriched in the GO entry to the number of all genes annotated to the GO entry. The greater the rich factor, the greater the enrichment.

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