Fig. 3: Differential gene expression between GPI(+) and GPI(−) HSPC subtypes in PNH patients.

A Dot plot showing gene set enrichment scores across HSPC subtypes comparing GPI(+) and GPI(−) HSPCs in patients with large PNH cell fractions by Gene Set Enrichment Analysis (GSEA). A color scale indicates mean normalized enrichment score (NES) differences between two groups, and dot sizes indicate false discovery rate (FDR) values. Non-significant pathways (FDR ≥ 0.20) are shown in grey. B A volcano plot of differentially expressed genes between GPI(+) and GPI(−) HSCs in patients with large PNH cell fractions. A horizontal dotted line and vertical dotted lines represent an adjusted P-value (padj) = 0.05 and absolute log2FC = 0.25, respectively. Genes upregulated and downregulated in GPI(+) HSCs compared to GPI(−) HSCs are highlighted in red and blue, respectively. C A dot plot of gene set enrichment scores across HSPC subtypes between GPI(+) and GPI(−) HSPCs in patients with small PNH cell fractions. D A volcano plot of differentially expressed genes between GPI(+) and GPI(−) HSCs in patients with small PNH cell fractions, generated as in (B). E Gene set module scores for the IFN-γ response pathway, activated HSC signature, the apoptosis pathway, and HLA class II genes in HSCs. Scores were shown for GPI(+) and GPI(−) HSCs in patients with small and large PNH cell fractions as violin plots, with mean module scores shown in bar charts at the bottom. P values were calculated with the two-sided unpaired Mann–Whitney U test. ETP, early T lineage progenitor, GMP granulocyte-monocytic progenitor, HSC hematopoietic stem cell and multipotent progenitor, ProB B lymphocyte progenitor, MEP megakaryocyte-erythrocyte progenitor, MLP multi-lymphoid progenitor.