Fig. 4

Weighted co-expression network analysis for identification and analyses of hub genes from the combined IDC and SLE datasets. A and D The left panel was the analysis of the scale-free fit index with multiple soft-thresholding powers (β), and the right panel was the analysis of the mean connectivity with multiple soft-thresholding powers. Both of them were based on the combined gene expression matrix of IDC(A)/SLE(D) from the five IDC/SLE studies. B and E Correlations between MEs and groups indicating the module-trait associations. Every row represented a ME, and every column represented the group. The groups of (B) contain control and IDC patients. The groups of (E) contain control and SLE patients. C and F The heatmaps with topology showing gene network of IDC(C)/SLE(F). The rows and columns represented gene list. The gene dendrogram and module assignment were shown at the left and top. G Venn diagram showing the total and intersected numbers of hub gene (|kME|≥ 0.8) in IDC and SLE. H PPI network of top 10 genes out of the 96 overlapping hub genes based on BC values obtained from Cytoscape plug-in Cytohubba. Colors represent BC values from high (red) to low (yellow). I GO and KEGG enrichment analysis based on the 96 hub genes shown in (G)