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. 2021 Jul 21;12(1):1808–1824. doi: 10.1080/21505594.2021.1948276

Figure 1.

Figure 1.

Differential expression analysis. (a) Principle component analysis of gene expression profiles using variance-stabilizing transformed (VST) counts of genes that passed filtering. (b) t-distributed stochastic neighbor embedding (t-SNE) plot of samples using enrichment scores of 64 cell types generated by cell type enrichment analysis via xCell webtool. TPM (transcripts per kilobase million) of genes that passed filtering were used for cell type enrichment analysis. (c) Enrichment scores of four immune cell types generated by cell type enrichment analysis. (d-h) Volcano plots of pairwise comparisons DEX VS CON (d), LPS VS CON (e), LPS+DEX VS CON (f), LPS+DEX VS DEX (g), and LPS+DEX VS LPS (h). Top 10 most significant genes in each comparison were determined by q-value and highlighted in the plot. (i) Heatmap constructed using LFC of genes in matched comparisons. Values were centered in the row direction. Abbreviation: CON, control; DEX: dexamethasone; LPS, lipopolysaccharide; aDCs, activated dendritic cells; CSM B-cells, class-switched memory B cells; Tregs, regulatory T cells; EN..38594, ENSSSCG00000038594; EN..32552, ENSSSCG00000032552