Differentiation defects in TS cortical neural progenitors. (A) Heatmap showing gene expression patterns in the black module and a barplot showing the corresponding module eigengene trajectory. (B) Boxplot comparing the module eigengene patterns between case cells vs. control cells at three experimental stages. (C) Barplot showing the log2 fold changes of the top 20 connected genes in the black module upon differentiation. Blue bars show the log2 fold changes in control samples, and pink bars represent the log2 fold changes in patient samples. (D) Differentiation-dependent gene expression changes in the patient progenitors. The differentiation-associated genes are categorized into four groups: (1) genes downregulated upon differentiation in controls but not in patients (top left); (2) genes that are upregulated upon differentiation in controls but not in patients (top right); (3) genes downregulated upon differentiation in patient cells but not in controls (bottom left); and (4) genes upregulated upon differentiation in patient cells but not in controls (bottom right). The log2 fold changes of the top 15 genes that show largest difference between cases and controls are shown in each group. The top enriched GO categories and KEGG pathways identified in each of the four gene groups are shown in the corresponding tables with enrichment P value attached.