Differentially expressed long noncoding RNAs and mRNAs in PC12 cells under lysophosphatidylcholine stimulation

Figures

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  Figure 1. Identification of lncRNAs in PC12 cell lines. (A) Flow chart of lncRNAs analysis; (B) Histogram representation of lncRNAs filtration; (C) Venne diagram of novel lncRNAs predicted based on CPC, CNCI and PFAM; (D) FPKM distribution analysis among four experimental groups; (E) FPKM density analysis among four experimental groups; (F) Pearson coefficient analysis four experimental groups.

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  Figure 2. Genomic characterization of lncRNAs in PC12 cell lines. (A) A pie chart illustrating the classification of lncRNAs derived from PC12; (B) Expression level distribution of lncRNAs and mRNAs derived from PC12 cells; (C) Representation of the transcript length distribution derived from PC12 cells; (D) Exon numbers of transcripts derived from PC12 cells; (E) Open reading frame (ORF) of transcripts derived from PC12 cells.

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  Figure 3. Pathway enrichment of lncRNAs co-expressed genes derived from PC12. (A) KEGG pathway analysis of the co-expressed genes of the annotated lncRNAs; (B) KEGG pathway analysis of the co-expressed genes of the novel lncRNAs. The horizontal axis represents enrichment factor and the vertical axis represents pathway. Different colors represent different adjusted p values. From purple to red, the adjusted p value changes from large to small and the degree of enrichment becomes more and more significant. The size of the dot represents the number of genes enriched into this pathway.

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  Figure 4. mRNAs and lncRNAs profiles from cells under different treatments and showed in Venn diagram and Heatmap analysis. (A, B): Venn diagram for mRNA and lncRNA pieceful. (C, D): Heatmap analysis for all differentially expressed mRNAs and lncRNAs.

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  Figure 5. Co-expression network of lncRNAs and mRNAs in PC12. The squared nodes represent lncRNAs, whereas the circled nodes represent mRNAs; the node size is denoted based on degree (higher values are mapped to the bright color) and the edge is denoted based on the Pearson values.

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  Figure 6. qRT-PCR validation of the sequencing results. The data showed that the relative expression level of genes fgf18, Pck2, Vcam1, Wnt5a and Fos in sequencing (black) and qRT-PCR experiments (gray). The relative expression level of genes here represents the fold change of genes by normalizing the 2−ΔΔCT value of each group by that of control group. The relative expression of fgf18, Pck2 and Vcam1 in sequencing and qRT-PCR were consistent: the expression of fgf18 and Pck2 were significantly up-regulated, while the expression of Vcam1 was down regulated (p < 0.05).