Extended Data Fig. 4: Leading-edge gene (LEG) analysis of iPD, GBA, LRRK2 G2019S, and prodromal cases at visit1.

(a) Bar plot of LEG analysis dissecting the key contributors in the shared HALLMARK_OXIDATIVE_PHOSPHORYLATION. Genes in this pathway, which are altered in all the four experimental groups, relate to mitochondrial respiration. (b) Venn diagrams illustrating the relationship of the genes in the HALLMARK_OXIDATIVE_PHOSPHORYLATION, which at visit 1 is deregulated in the four studied experimental groups (i.e. iPD, GBA and G2019S LRRK2 carriers, and prodromal cases). (c) Bar plot of LEG analysis in the shared HALLMARK_MYC_TARGETS_V2. Genes in this pathway, which are altered in all the four experimental groups, relate macromolecular synthesis linked to transcription and translation and nucleic acid metabolism. (d) Venn diagrams illustrating the relationship of the genes in the HALLMARK_MYC_TARGETS_V2, which at visit 1 is deregulated in the four studied experimental groups. (h) GSEA against GO-BP, KEGG, WikiPathways confirms results obtained against the Reactome database, indicating that deregulated processes largely relate to macromolecular synthesis linked to transcription and translation. (e) UpSet plot and (f) heatmap of the enriched GSEA against the Reactome compendium show the 13 shared pathways among the experimental groups, which were all down-regulated. (g) Shared LEG analysis of the 13 Reactome shared pathways largely identifies biological processes relative to translation and RNA metabolism. In the heatmaps, up- and down-regulated pathways are respectively in red and blue; p.adj<0.05. NES: normalized enrichment score. In GSEA, enrichment significance was assessed using a one-sided, permutation-based test on the NES, as implemented in the fgseaMultilevel() function, which employs an adaptive multilevel Monte Carlo algorithm and includes multiple comparison correction to estimate low p-values efficiently. In ORA (a, c, g, i), p-value was calculated with Fisher’s exact test and corrected for multiple hypotheses with the Benjamini-Hochberg procedure.