Identification of Lncrna-Mrna Networks in Hepg2 Cells upon ATP7B Knockout and Copper Accumulation

Figures

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  Fig. 1:. The differentially expressed lncRNAs and genes in HepG2 cells in response to ATP7B knockout (KO) and copper accumulation. A and B, the Volcano plots of the differentially expressed lncRNAs and genes in HepG2 cells upon ATP7B KO and ATP7B KO + Cu, respectively, compared with wild-type (WT) cells. FC, fold change. FDR, false discovery rate. Red for upregulation and green for downregulation. C and D, the hierarchical clustering heatmaps of the differentially expressed lncRNAs and genes in samples, respectively. Red and green colors note high and low expression, respectively

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  Fig. 2:. Mfuzz clustering analysis of the differentially expressed genes and lncRNAs. A, the Venn diagram showing the number of differentially expressed lncRNAs and genes in HepG2 cells upon ATP7B knockout (KO) with and without Cu toxicity. B, four Mfuzz clusters of genes with different expression patterns on ATP7B KO and Cu toxicity. WT, wild-type

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  Fig. 3:. Results of functional enrichment analysis for the differentially expressed genes in clusters 1 and 4. A and B, bubble diagrams showing the significantly enriched biological processes and pathways associated with the genes in clusters 1 and 4, respectively

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  Fig. 4:. The lncRNA-mRNA regulatory networks of the genes/lncRNAs in clusters 1 and 4, respectively. A and B, the lncRNA-mRNA regulatory network involving the differentially expressed genes/lncRNAs in cluster 1 and cluster 4, respectively. All the lncRNA-mRNA interaction pairs have high Pearson correlation coefficients (>0.9). LncRNAs are indicated by squares, and genes in clusters 1 and 4 are noted by diamonds (upregulation) and cycles (downregulation), respectively

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  Fig. 5:. The biological processes and pathways associated with the differentially expressed genes in the lncRNA-mRNA networks of clusters 1 and 4. Bubble diagrams showing the significantly enriched biological processes (n=16) and pathways (n=9) associated with genes in the lncRNA-mRNA networks of clusters 1 and 4

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  Fig. 6:. The lncRNA-gene-pathway network. The final lncRNA-gene-pathway network consists of 13 lncRNAs (empty squares), 10 genes (cluster 1: diamonds, and cluster 4: circles), and two pathways (yellow squares). Involvement in pathways is shown by a green line