Fig. 2

Functional annotation of DEGs and their relationship to CHD8-binding. a Venn diagram of DEGs from CHD8 ^+/− in iPSC-derived NPCs and neurons. b qRT-PCR validation of seven DEGs, using β2-microglobulin (β2M) as a reference gene to calculate relative expression levels. The qPCR was carried out on neurons derived from two control samples and the two CHD8 ^+/− clones (the same samples used for the RNA-seq). Each was normalized against another control sample. Samples were analyzed in triplicate. The graph shows the fold change for each sample relative to the neutral control, error bars show the +/− standard deviation. The fold changes were highly significant: SMARCA2, p = 9.7E-7; WNT7A, p = 6.1E-9; HMGA2, p = 4.4E-6; TESC, p = 0.003; TCF4, p = 4.4E-5; TGFB3, p = 5.5E-6; DDR2, p = 6.2E-8 (two-tailed Student’s t test). c Percentage of CHD8-binding genes in all protein-coding, upregulated, and downregulated genes in NPCs, ranked by their expression values (FPKMs) in WT NPCs. Asterisks (“*”) mark the groups of genes showing a significant difference in the proportions of genes with CHD8 binding by comparing DEGs with all protein-coding genes (binomial test, two-tailed, p < 0.05). d Representative-enriched GO terms (top) and canonical pathways (bottom) among DEGs, as reported by DAVID and IPA, respectively. The red color in each cell corresponds to the −log₁₀(p value), corrected by Benjamini-Hotchberg method (color scale on the left and only terms with p < 0.05 were shown)