On the pathway level, the NOS1- and CREB-pathways as well as the pathway regulating PGC1α (among others) were significantly inactivated in PD-patient derived neurons (p < 0.05, FDR < 0.25, n = 8 CTRL neurons and 7 PD neurons, Figs. 2d and e and Additional file 5: Table S3). Here, PPARGC1A is linked to Parkinson disease.