MPN platelet proteome distinguishes disease phenotype. (A) Unsupervised principal component analysis of normalized platelet protein expression adjusted for age, sex, treatment (antiplatelet and cytoreduction), and experimental batch. PC1 and PC2 colored by MPN subtype; and each contrasted with controls (n = 40, yellow): ET (n = 59, light green), PV (n = 41, blue). The first 2 principal components account for 26% of total variance in the data. (B-C) Volcano plots (2 panels of ET, PV) of differential protein expression showing log2 fold change vs statistical significance (negative log10 of P values) of each gene. Significant upregulated and downregulated genes are those with P values (false discovery rate [FDR]) ≤.05 and absolute value of fold changes ≥1.5. (D) Hierarchically clustered heat map of the top 10 differentially expressed proteins (FDR <0.01) from control vs MPN patient samples. Colored annotation is provided to indicate MPN subtype, mutation status, and sex. Rows indicate gradation in expression on a yellow (low) to orange (high) scale. Columns indicate sample type from controls, ET, and PV. (E) Pathway-enrichment analysis of proteins with MPN subtype–specific expression (color indicated; yellow ET, and light green PV). Each point represents a pathway; the x-axis gives the normalized enrichment score, which reflects the degree to which each pathway is overrepresented at the top of the ranked list of differentially expressed proteins, normalized to account for differences in gene set size and in correlations between gene sets and the expression data set. The y-axis lists the detail-level node of the most enriched pathways; solid lines mark gene set enrichment analysis–recommended¹¹ Bonferroni-corrected statistical significance criterion of FDR <0.25 for exploratory analyses.