Fig. 6

Network analysis of regulated proteins involved in the Parkinson’s disease pathway. a Hierarchical clustering of differentially expressed proteins. The color coding shows the relative abundance based on the Z-score transformation. Two different clusters of proteins were subjected to pathway enrichment analysis. b The pathway analysis was performed using DAVID Bioinformatics Resource (https://david.ncifcrf.gov) with the Benjamini–Hochberg false discovery rate (FDR) ≤ 0.05 (PMID: 19033363). Empty bar: mutation-corrected isogenic iPSCs; blue bar: LRRK2 p.G2019S iPSCs. c Each circle represents one regulated protein, and different colors represent the distinct sub-pathway inside the PD pathway: green, ubiquitination; yellow, proteasome degradation; blue, oxidative phosphorylation; purple, apoptosis; and pink, synaptic vesicle trafficking. Filled circles indicate that the protein level was increased in LRRK2 G2019S iPSCs, whereas down-regulated proteins are indicated as clear circles