Table 1.
The primer sequences used in this study.
Fig 1.
Identification of expressed lncRNAs in IgA nephropathy.
A. Workflow of lncRNA prediction and analysis in this research. B-C. Venn diagram showing the number of detected lncRNAs. The known and new predicted lncRNAs were detected. (Expressed at least 1 sample with FPKM > 0) D. Principal component analysis (PCA) based on FPKM value of all mRNA. The ellipse for each group is the confidence ellipse. E. Principal component analysis (PCA) based on FPKM value of all lncRNAs. The ellipse for each group is the confidence ellipse.
Fig 2.
Analysis of differential expression of lncRNAs and mRNAs in IgA nephropathy.
A. Principal component analysis (PCA) based on FPKM value of the DEmRNA. The ellipse for each group is confidence ellipse. B. Principal component analysis (PCA) based on FPKM value of the DElncRNA. The ellipse for each group is the confidence ellipse. C-D. Volcano plot showing all differentially expressed genes (DEGs) and lncRNA (DEGs) between the two groups with DEseq2. FDR< 0.05 and FC (fold change) ≥ 2 or ≤ 0.5. E. The Heatmap showing the expression profile of the most significant top30 DElncRNA (up15 plus down 15) F-G. Bar plot showing the most enriched GO biological process results of the up-regulated and down-regulated DEGs. H. Scatter diagram showing DElncRNAs enrichment by Patient compared with Health samples and its number of co-expressed DEmRNAs. Red points denote up-regulated lncRNAs involved in co-expression pairs and blue points denote down-regulated lncRNAs. Cutoffs of p value < 0.01 and Pearson coefficient > 0.9 were applied to identify the co-expression pairs. I. Bar Diagram exhibiting the most enriched GO biological process results of the DElncRNA coexpressed DEmRNA.
Fig 3.
Cis-regulatory TFs of DE lncRNAs associated with IgA nephropathy.
A. Scatter diagram showing log2 FC of DE lncRNAs by Patient compared with Health samples and its cis-regulatory genes. B. Heatmap showing lncRNA and cis-regulatory genes C. Bar plot showing the most enriched GO biological process results of the DElncRNA cis-target DEGs. D. Venn diagram showing the overlap TFs and DElncRNA cis-target DEGs. E. Venn diagram showing the overlap pairs number of cisTF-target pairs from database and cisTF-DEG coexpression pairs. F. Bar plot showing the most enriched GO biological process results of the cis TF target DEGs. G. Network diagram showing the cis TF target DEGs regulated by cis TF and DElncRNA.
Fig 4.
Exhibition of the differential expression of lncRNAs, cisTF and targeted DEGs in Patient and Health Samples.
A. The Heatmap showing the expression profile of the lncRNA and cis TF in Fig 3.G B. The reads distribution showing lncRNA NQO1 − DT and its regulated cis TF NFAT5. Boxplot showing the expression of lncRNA, cis TF and target DEGs. * P-value < 0.05, ** P-value < 0.01, *** P-value < 0.001. C. The reads distribution showing lncRNA RP5 − 1057I20.6 and its regulated cis TF VDR. Boxplot showing the expression of lncRNA, its regulated cis TF and target DEGs. * P-value < 0.05, ** P-value < 0.01, *** P-value < 0.001.
Fig 5.
Relative expression levels of lncRNAs, transcription factors (TFs) and mRNAs in validation cohort.
(The experiments were repeated three times. Student’s t test was used to analyze the statistical significances of differences between two groups).
Fig 6.
Transcription factors VDR and NFAT5 is different expression in IgAN and healthy control.
A. Immunofluorescence analysis showing that VDR expression level in healthy control (HC) was higher than in IgAN. B. Immunofluorescence analysis showing that NFAT5 expression level in IgAN was higher than in healthy control.