Extended Data Fig. 4: miRNA expression marker validation using 1,440 microarray samples of the independent NCER-PD cohort.

a, Scatter-plot of miRNA effect size (n = 416, black circles) between total PD and controls obtained from sncRNA-seq (PPMI) and microarray (NCER-PD). The smoothed trendline (orange) is enclosed by light grey bands showing the standard error. Center of measurements were computed by LOESS fitting. Standard errors correspond to the 95% confidence intervals. One-dimensional histograms are shown on the right and top for sncRNA-seq results and microarray results, respectively. b, Similar to a but restricted to the effect sizes between gPD and unaffected genetic carriers from the sequencing study. c, Venn-diagram for the most significant overlap between the miRNAs detected with sequencing or microarray as computed by DynaVenn. Input miRNAs were sorted by decreasing AUC for iPD vs. healthy controls in case of the sequencing data and iPD vs. controls in case of the microarray data. d, The most significant overlap obtained (adj. p = 3.39 × 10⁻¹⁸) at n = 222 shown in c as a function of the position in the DynaVenn input list. P values were computed using a two-sided hypergeometric test and subsequently corrected using the BH-FDR procedure at an α-cutoff of 0.05. e, Two-dimensional representation of the entire P value search space investigated by DynaVenn for all possible overlaps of miRNAs from the sequencing and microarray studies. P values were computed as described in d. f, Results of a miEAA 2.0 over-representation/enrichment analysis using the miRNAs determined for the most significant overlap displayed in c. The x-axis shows the BH-FDR adjusted P value for each category on the y-axis. Integers on the right display the number of hits observed per category or biological pathway. The color shading corresponds to the number of hits per category. P values were computed using a two-sided hypergeometric test and subsequently corrected using the BH-FDR procedure at an α-cutoff of 0.05.