Fig. 2

mRNA expression profiling of PD-patient derived cell lines (a) Heatmap and hierarchical clustering based on the TOP2000 variable genes on mRNA expression data. Hierarchical clustering separates the samples by cell type (fibroblast, iPSC/ESC or neuron). PD-patient derived cells (shades of salmon) are not separated from control-patient derived cells (shades of grey) and iPSCs are not separated from ESCs (gold). b Summary of differential expression analysis results as calculated by DESeq2 between control- and PD-patient derived cells. A significant number of deregulated genes is only present in neurons, but not in fibroblasts or iPSCs. c WNT3 is differentially expressed between control- and PD-patient derived cells as judged by real-time PCR (two-sided Mann-Whitney test, p < 0.05). Shown are means + SD. d The NOS1- and CREB-pathways as well as the pathway regulating PGC1α (as defined by c2.Biocarta) are significantly inactivated in PD-patient derived neuronal cells (p < 0.05 and FDR < 0.25 as calculated by GSEA). e Heatmap of CREB pathway genes that show a core enrichment in the GSEA analysis based on rlog normalised expression values of the midbrain neurons