Fig. 2: Cell type-specific changes in gene expression at E14.
From: MYT1L deficiency impairs excitatory neuron trajectory during cortical development
A Summary plot showing the numbers of nuclei and genes detected in each cluster (left). Bar plot (middle) displays the number of differentially expressed genes (DEGs) upregulated in WT (red) or KO (blue) conditions (n = 3 biological replicates per condition). DEG burden analysis (right) shows the distribution of DEGs per cell type, normalized by the number of nuclei in each cluster. Statistical significance was assessed using a two-sided Mann-Whitney U test with Benjamini-Hochberg correction for multiple corrections (*FDR adjusted p < 0.05). Box plots show median (center line), interquartile range (box), and whiskers extending to 1.5 times the interquartile range. B MYT1L gene dose-dependent expression patterns of DEGs in Im ExN_2 and L5-6 ExN_1 clusters, categorized as MYT1L-activated (decreased expression in KO) and MYT1L-represssed (increased expression in KO). Box plots show median, interquartile range, and whiskers extending to 1.5 times the interquartile range. Dot plots showing enriched GO biological processes terms in MYT1L-repressed (C) and MYT1L-activated (D) DEGs. Overrepresentation of genes within GO terms was determined using a one-sided hypergeometric test, with p values adjusted for multiple testing using the Benjamini-Hochberg method. E Plot showing the frequency distribution of annotated protein classes among the DEGs. F Heatmap displaying identified regulons (columns) for each WT cluster (rows), colored by the Regulon Specificity Score (RSS). RSS measures the specificity of each regulon’s activity for each cluster. Cluster classes are annotated on the right, and differentially expressed regulons are annotated in each column. G Representative plots showing the ranked Regulon Specificity Score plots for Im L5-6 ExN_1, L5-6 ExN_1, and Sst InhN clusters. Differentially expressed regulons are highlighted in red and labeled on the plot.
