Fig. 4

Transcriptomic analysis of genes with differential expression in affected subject-derived NPCs, relative to unaffected controls. a Hierarchical clustering of RNA-seq data from the cExN NPCs identified differentially expressed genes (DEGs) with shared expression in the AP and IS that differed from that in the UM. Relative expression is also shown for the UC, for a full cross-sample comparison (P < 0.05, fold-change > 2; n = 4 biological replicates from one clonal line for each subject, and one clonal line for the UC). b-d Ingenuity Pathway Analysis (IPA) of these cExN NPC DEGs defined disease- and function-associated gene ontology (GO) terms and identified gene networks associated with the (c) ‘behavior’ and (d) ‘behavior and developmental disorder’ GO terms. e Hierarchical clustering of RNA-seq data for the cIN NPCs identified DEGs with shared expression in the AP and IS, that differed from that in the UM. Relative expression is also shown for the UC, for a full cross-sample comparison (P < 0.05, fold-change > 2; n = 4 biological replicates from one clonal line for each subject, and one clonal line for the UC). f-h IPA analysis of these cIN NPC DEGs defined (f) disease- and function-associated GO terms and identified gene networks associated with (g) ‘behavior’ and (h) ‘psychological disorder’. Within each network, red symbols indicate upregulated genes and green symbols indicate downregulated genes, while color intensity indicates the relative degree of differential expression