Extended Data Fig. 8: Characterization of the cells carrying mCAs.
From: Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution
(a) Fractions of the mutant cells carrying each copy number alterations (CNA) event (left) and those of the mutant cells carrying each copy-neutral loss of heterozygosity (CN-LOH) event colored by setting of sequencing (right). (b) Heatmaps showing the in-sample odds ratios of each subcluster (L2) containing the CNA cells in CH01 (top) and CH05 (bottom). (c) Differential gene expression (DEG) analysis between the somatically mutant and normal cells for 1p_Loss monocytes (left), 15q_Gain monocytes (middle), and 17q_Gain B cells (right). DEGs are colored in light blue (downregulated) or pink (upregulated), and DEGs on the corresponding chromosomal regions are colored in navy or red. DEGs were significant if they satisfied FDR (adjusted P values via the Benjamini-Hochberg method) < 0.05 and log2 fold change > 0.25 (in CH01) or 0.5 (in CH05). (d-g) Top ten enriched biological pathways of the downregulated DEGs in 1p_Loss monocytes (d), the downregulated DEGs in 15q_Gain monocytes (e), the downregulated DEGs in 17q_Gain B cells (f), and the upregulated DEGs in 17q_Gain B cells (g). Dot color indicates the statistical significance of the enrichment (adjusted P values via the Benjamini-Hochberg method), and dot size represents gene count annotated to each term.
