Fig. 4: Differential gene expression in cell clusters in LPS + PA14 versus PA14 mice. | Nature Communications

Fig. 4: Differential gene expression in cell clusters in LPS + PA14 versus PA14 mice.

From: Neutrophils and galectin-3 defend mice from lethal bacterial infection and humans from acute respiratory failure

Fig. 4

a Volcano plot of genes differentially expressed genes in the DESeq2-based pseudo-bulk analysis of LPS + PA14 versus PA14 cells. Red points indicate significance in both fold-change (log2FC > 0.5) and Benjamini-Hochberg (BH) adjusted p-value (p < 0.05). b Stacked violin plots highlighting select genes that were found to be differentially expressed between the two conditions (LPS + PA14 versus PA14). c A dotplot comparing the expression levels of core genes of select pathways of interest enriched in LPS + PA14 against PA14 cells. The size of the dot indicates the gene ratio, and the color of the dot shows the normalized enrichment score (NES). The dendrogram in the y-axis represents the clustering of the pathways by the NES. d Feature plot visualizing expression of Lgals3, and the color represents the average expression level across cell types. e Chord diagrams showing the pathways of interest from the GSEA. In each diagram, enriched clusters are shown on the right and genes contributing to the enrichment are shown on the left. Genes are colored by log fold-change value, and the color of the chords represent distinct pathway/ontology Terms.

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