Extended Data Fig. 6 |. Differentially regulated genes, canonical pathways, and upstream regulators in CD8+ T cells.
a, Heatmap of DE genes for each COVID-19 sample colored by average log(fold-change). DE genes were calculated by comparing gene expression of individual COVID-19 samples with gene expression of all healthy controls using Seurat’s implementation of the Wilcoxon rank-sum test. Only DE genes with a two-sided p value<0.05 adjusted for multiple comparisons by Bonferroni’s correction are shown. These DE genes were used to identify b, enriched canonical pathways and c, upstream regulators, both colored by z-score, using Ingenuity Pathway Analysis (IPA). The (a) 50 genes, (b) 14 pathways, or (c) 50 regulators with the highest absolute average log(fold-change) or z-score across all donors are labeled. Genes with a net positive average log(fold-change) or z-score are labeled in red; genes with a net negative average log(fold-change) or z-score are labeled in blue. All (b) pathways and (c) upstream regulators are statistically significant by IPA’s implementation of Fisher’s exact test at a right-sided p < 0.05. Number of cells: C1 A – 563, C1 B – 904, C2 – 176, C3 – 1,437, C4 – 432, C5 – 183, C6 – 80, C7 – 102; cells from all healthy controls (n = 2,885 cells) were used to generate comparisons with each COVID-19 sample.