FIGURE 4.

Gene regulatory network inference using weighted gene co-expression network analysis (WGCNA) reveals cell type-specific modules. (A) Topological overlay map (TOM) plots demonstrate clustering of potential gene regulatory networks consisting of co-expressed genes termed modules arrayed along the horizontal and vertical axis. The more red a box is, the higher the Pearson correlation coefficient is between the respective modules. TOM plots are shown for the scRNA-Seq (LEFT) and snRNA-Seq (RIGHT) datasets. (B) Adjacency plots display highly correlated modules in the scRNA-Seq dataset (LEFT panel). The more red a box is, the more similar the 2 intersecting modules are to each other. Note that in the snRNA-Seq dataset (RIGHT panel), the correlation between modules is minimal. Using known cell type-specific marker genes, we focused on the cell type-specific modules identified in the scRNA-Seq dataset. (C) Cell type-specific WGCNA modules were then projected onto the scRNA-Seq feature plot to demonstrate aggregate cell type-specificity of these WGCNA modules for the three major cell types (marginal, intermediate, and basal cells). The more red a dot is in the feature plot, the greater the aggregate expression of the cell type-specific modules in that given cell.