Fig. 4

Cluster-associated alterations in HSPCs of ITP patients. a Boxplot showing the fraction of each HSPC cluster in ITP (blue) and HC (red) samples. The p values were calculated using two-tailed Student’s t test; *p < 0.05. b Differential gene expression (DGE) analysis showing up- (red) and down- (blue) regulated genes in ITP across the 15 HSPC clusters. A log-transformed fold change absolute value greater than 0.25, the minimum percentage >0.25, and adjusted p value <0.05 were used to define significantly differential expression genes (DEGs) in each cluster. c Correlation between ITP and HC transcriptomes in preB3. Each axis represents the mean expression level in the HSPC subset and each point represent a single gene. Red points represent significantly upregulated genes in ITP, blue points represent significantly downregulated genes in ITP, and gray points represent non-DEGs. A log-transformed fold change absolute value >0.25, the minimum percentage >0.25, and adjusted p value < 0.05 were used to define significance. d Representative GO: BP terms were relatively enriched in preB3 from ITP versus HC. e GSEA plots showing pathways enriched in preB3 from ITP versus HC. NES normalized enrichment score, FDR false discovery rate. f Bubble heat map of ligand-receptor interactions between preB3 and Mk/Ery-lineage cells. Interaction pairs with ITP (p < 0.05) were selected. ITP and HC are presented separately. Dot size indicates logarithmic transformed p values (permutation test). Color indicates the scaled mean expression levels of ligand and receptor molecules in the corresponding cell subpopulations. The upper panels represent interaction pairs specifically in ITP (p ≥ 0.05 in HC). The lower panel represents interaction pairs specific for both ITP and HC (p < 0.05 in HC). See also Supplemental Fig. 10. g Heat map of the area under the curve (AUC) scores of TF motifs estimated per sample in preB3 using SCENIC. A log-transformed fold change value >0.25, and adjusted p value < 0.05 were used to define significantly differential expression TFs. Significant TF motifs shared by at least two ITP samples would be selected for visualization. See also Supplemental Fig. 11