Fig. 4
Gene coexpression modules and predicted secreted protein (PSP) genes that were associated with conditions and cellular states in ASCs. A Dendrogram showing the gene coexpression modules M1–M8 that were identified in ASCs through high-dimensional weighted gene coexpression network analysis (hdWGCNA). B Gene coexpression network of the gene modules. Each dot represents a gene. The hub genes were determined by identifying the top 25 genes ranked by eigengene-based connectivity (kME) in each module. The top five hub genes of each module are shown. C Condition-associated gene modules identified by differential module eigengene analysis. Two-tailed Wilcoxon rank sum test. The significance threshold was set to an absolute log2 (fold change) value > 0.75 and a P-value adjusted for multiple testing < 0.05. D Dot plot showing the expression of harmonized module eigengene (hME) of each module across ASC subclusters. E UMAP plots showing the expression distribution of hME for modules M1 and M3. F Network plot showing the hub genes of the modules M1 and M3. G Dot plots showing the expression patterns of upregulated or downregulated PSP genes in CD55high ASCs compared with CD55low ASCs. The top 100 differentially expressed PSP genes are shown. Likelihood-ratio test implemented in Seurat. The threshold was set to an absolute log2-fold change > 0.25 and an adjusted P-value < 0.05