Molecular mechanism analysis of m6A modification-related lncRNA-miRNA-mRNA network in regulating autophagy in acute pancreatitis

Figures

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  Figure 1.. The flow chart of m6A modification-related lncRNA-miRNA-mRNA network in regulating autophagy and affecting the development of AP screened through bioinformatics technology.

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  Figure 2.. Multi-dataset merging and batch effect removal. (A) Sample distribution of three RNA-seq datasets before batch effect removal. A, sample distribution of three RNA-seq datasets before batch effect removal. (B) Sample distribution of three RNA-seq datasets after batch effect removal. (C) The volcano map of differential analysis of the merged dataset, red represents upregulation, green represents downregulation, black represents insignificant difference. (D) The heatmap of differential analysis of the merged datasets GSE3644 (control = 3, AP = 3), GSE109227 (control = 4, AP = 4), GSE121038 (control = 5, AP = 6).

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  Figure 3.. m6A-lncRNA network construction. (A) The expression heatmap of 32 lncRNAs in the merged dataset. (B) Correlation analysis of the expression of 15 m6A genes and 32 lncRNAs. *p < .05. **p < .01. ***p < .001. The X-axis indicates lncRNAs, and the Y-axis indicates m6A genes. (C) The Venn diagram of intersection of lncRNAs significantly related to m6A and differentially expressed genes in AP. (D) The m6A-lncRNA network of 9 candidate lncRNAs and 11 related m6A genes was constructed. The degree value gradually decreased clockwise from Ythdf1. Red represents upregulation, green represents downregulation, the square represents m6A genes, the triangle represents upregulated lncRNAs, and V-shape represents downregulated lncRNAs.

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  Figure 4.. Functional enrichment analysis of autophagy genes. (A) The Venn diagram of intersection between differentially expressed genes in AP and screening results from GeneCards and CTD database. (B) The Venn diagram of intersection of disease genes and autophagy genes. C, GO-MF (red), GO-CC (blue) and GO-BP (green) analysis results of 21 autophagy genes. Column height indicates enrichment significance. (D) The KEGG analysis results of 21 autophagy genes. The color of the dots represents the p-value, and the dot size represents the number of enriched targets. The X-axis represents the number of enriched targets, and the Y-axis represents the pathway name.

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  Figure 5.. Screening of upstream miRNAs of the 21 candidate autophagy genes. (A) Upstream miRNA prediction of 16 upregulated candidate autophagy genes. (B) Upstream miRNA prediction of five downregulated candidate autophagy genes. The numerical value in the figure represents the predicted number of miRNAs, and the connecting line represents the jointly targeted miRNAs.

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  Figure 6.. The regulatory network of 16 upregulated candidate autophagy genes and their targeted binding miRNAs. Red represents upregulation, the square represents genes, the ellipse represents miRNAs.

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  Figure 7.. The regulatory network of 5 downregulated candidate autophagy genes and their targeted binding miRNAs. Green represents downregulation, the square represents genes, the ellipse represents miRNAs.

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  Figure 8.. lncRNA-miRNA-mRNA network construction. (A) Upregulated lncRNA-mediated lncRNA-miRNA-mRNA regulatory network. (B) Downregulated lncRNA-mediated lncRNA-miRNA-mRNA regulatory network. In the figure, red represents upregulation, green represents downregulation, the square represents genes, the ellipse represents miRNAs, the triangle represents upregulated lncRNAs, and V-shape represents downregulated lncRNAs.