Fig. 4: Differential expression analysis between del(5q) and non-del(5q) cells within MDS samples exposes transcriptional similarities.

A Heatmap representing the differentially expressed genes (Benjamini–Hochberg-adjusted p-values < 0.05 and |logFC|>2) between del(5q) and non-del(5q) cells within each hematopoietic progenitor. The heatmap was created by combining n = 4 del(5q) MDS patients and generating pseudobulks per cell type. The two-sided edgeR’s Likelihood Ratio Test was used to calculate p-values. The exact number of biologically independent replicates (del(5q) and non-del(5q) progenitor cells), as well as the specific p-values for each differentially expressed gene can be found in the Source Data. B Dotplot representing statistically significant biological processes and pathways (Benjamini–Hochberg-adjusted p-values < 0.05) for differentially expressed genes obtained in del(5q) versus Healthy and the non-del(5q) versus Healthy contrasts. The one-sided hypergeometric test was used to calculate p-values. Del(5q) and non-del(5q) cells were derived from n = 4 del(5q) MDS patients, whereas healthy cells were derived from n = 3 healthy donors. Biologically independent replicates (del(5q), non-del(5q) and healthy progenitor cells) used for each comparison are specified in the Source Data. C–E Histograms representing the activity score in all the cells separated by conditions. Some regulons behaved similarly in the MDS samples (non-del(5q) and del(5q) cells) compared to healthy cells (C), while other regulons behaved differently in the three different conditions (D). Some inferred regulons had an activity score on the MDS samples, while lacking on the healthy samples (E).