Extended Data Fig. 5. GO enrichment analysis in patient Mutant and Corrected cells.
a, Gene Set Enrichment Analysis (GSEA) plots showing the enrichment of up and downregulated genes in the set of genes annotated as GO “central nervous system neuron development”. Genes are ordered based on the differential expression values obtained from DESeq2. P-values were calculated using Fisher’s exact test (two-sided). Exact p-values and multiple testing adjusted p-values are indicated. b, GO enrichment analysis showing GO terms that are upregulated in Mutant samples (enriched in Mutant) and downregulated in Mutant samples (enriched in Corrected) at day 14, (c) day 30, (d) day 60 and (e) day 90. b-e: P-values were calculated using goseq and adjusted for multiple testing. f, qPCR analysis of WNT1, WNT3a and AXIN2 mRNAs at day 7 (left), 14 (middle) and 30 (right) of neuronal differentiation in Mutant and Corrected lines confirms RNA-seq data. Data are represented as mean ± SD of 3 (WNT1 day 7 and day 14, WNT3a day 7 and day 14 and AXIN2 day 14) and as mean ± SD of 4 (AXIN2 day 7 and WNT1, WNT3a and AXIN2 day 30) independent experiments. The p-values by two-tailed unpaired Student’s t-test are indicated. P < 0.05 was considered statistically significant.