Fig. 3: GRNs that establish cell identities.
From: Molecular and cellular dynamics of the developing human neocortex
a, The minimum–maximum-normalized TF expression levels, region-based AUC scores and gene-based AUC scores of selective eRegulons across cell types. b, GRNs of selective eRegulons in three distinct cell types (RG-vRG, EN-L4-IT and IN-MGE-PV). TF nodes and their links to enhancers are individually coloured. The size and transparency of the TF nodes represent their gene expression levels in each cell type. ACC, accessibility; GEX, gene expression; R2G, region to gene. c, UMAP plots of cells belonging to EN lineages, showing the nine trajectories. Cells are colour coded by types, regions, age groups or pseudotime. d, Standardized gene-based AUC scores of six eRegulon modules along the trajectories of EN lineages. eRegulons are colour coded by neuronal trajectories. Thick, non-transparent lines represent the average AUC scores of each module in each trajectory. e, Gene Ontology enrichment analysis for target genes of individual eRegulon modules. Empty space indicates adjusted P > 0.05. Statistical analysis was performed using one-sided hypergeometric tests; nominal P values were adjusted using the Benjamini–Hochberg method. f, BPs during EN differentiation. g, Trajectories of four IT neuron lineages. h, Differentially expressed genes between V1-specific and common EN-L4-IT neurons. Statistical analysis was performed using likelihood ratio tests; nominal P values were adjusted using the Benjamini–Hochberg method. i, Representative eRegulons (activators) involved in trajectory determination at BPs. j, UMAP representation of representative eRegulons involved in trajectory determination at BPs.
