Fig. 3
Identification and analyses of DEGs from the combined IDC and SLE datasets by differential gene analysis of the limma R package. A and D Principal component analysis of five IDC(A)/SLE(D) datasets before (upper panel) and after (low panel) elimination of batch effects. B and E The volcano plots of the genes from the combined matrix from five IDC(B)/SLE(E) studies after eliminating batch effects, and DEGs (p-value < 0.05) were plotted in red (log2 (FC) > 0.5) and blue (log2 (FC) < -0.5). C and F The heatmap of the DEGs in IDC(C)/SLE(F) expression in normal controls and IDC/SLE patients. The DEGs in IDC/SLE were the DEGs shown in (B)/(E) with red or blue. G. Venn diagram showing the total and intersected numbers of DEGs in IDC and SLE. H PPI network of top 10 genes out of the 58 overlapping DEGs based on BC values obtained from Cytoscape plug-in Cytohubba. Colors represent BC values from high (red) to low (yellow). I GO enrichment analysis based on the 58 DEGs shown in (G). J KEGG enrichment analysis based on the 58 DEGs shown in (G)