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. 2023 Jul 5;14:3956. doi: 10.1038/s41467-023-39652-6

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a Volcano plot showing differential gene expression analysis of blood transcriptome from PPMI subjects. Select RNAs that are also significantly up- or downregulated in the PD striatum (caudate or putamen) are labeled. Controls (n = 195), PD (n = 479). Only significantly (FDR <0.05) changed (log₂FC >0.1 or <−0.1) RNAs in PD blood (determined by moderated t-tests with multiple test corrections using limma) are colored according to direction. Blue asterisk indicates log₂FC < −1. b Cumulative distribution function plots show that top (FDR <0.05, log₂FC >0.5, or log₂FC <−0.5) changed RNAs in the PD caudate and putamen (n = 35 each) are collectively differentially expressed in the same direction in blood from controls (n = 195) and PD (n = 479) subjects in the PPMI cohort. p values were calculated using two-sided Kolmogorov–Smirnov tests. c RNA expression box plots showing log₂(cpm) for select RNAs significantly changed in the striatum (controls (n = 40), PD (n = 35)), and blood (PPMI) in controls (n = 195) and PD (n = 479) subjects. p values were determined by two-sided Wilcoxon tests. C control. d Volcano plot shows significantly (FDR <0.05) changed GO terms in PD blood compared to controls. Select top GO terms are labeled. p values and FDRs are determined by moderated t-tests and multiple test corrections using limma. e Gene set enrichment scores of the top downregulated GO term (extrinsic component of postsynaptic density membrane) in PD blood correlate with disease progression, based on Hoehn and Yahr scale and MDS-UPDRS III motor scores. C-Controls (n = 195), PD (Hoehn and Yahr 1: n = 93, 2: n = 249, 3: n = 26; MDS-UPDRSIII 0-30: n = 224, 30–80: n = 144) p values were obtained from the Wilcoxon test. Only significant comparisons as determined by two-sided Wilcoxon tests are shown. Box plots show lower and upper hinges corresponding to the first and third quartiles (representing the 25th and 75th percentile, respectively). Whiskers extend from the hinge to the 1.5 × inter-quartile range. The center line indicates the median. Source data are provided as a Source Data file.