Gene regulatory network (GRN) inference using WGCNA and SCENIC.

(A) WGCNA analysis of cHCs and endogenous HCs, showing the correlation of each cell type and the expression pattern of eigengenes in each module. Each spike represents one cell of the cell types indicated below. (B) Correlation matrix depicting the correlation coefficients of different modules, with all seven modules included and self-comparisons removed from the graph. The size of the box and its color gradient indicate the correlation coefficient. (C) SCENIC identified cell-type-specific GRNs during SC-to-cHC conversion. The binary regulon activity matrix shows correlated regulons (absolute correlation > 0.3) active in at least 1% of cells. Cells are colored according to cluster identity, and genes are colored based on expression level. Regulons exceeding a manually adjusted AUC threshold are shown in black, while inactive regulons are white. Each stage of the conversion is shown at the top of the graph in different colours. (D) Venn diagram displaying the five overlapping key regulators identified by both WGCNA turquoise module (cHC3) and SCENIC in cHC2/3, compared to regulons in OHCs.