Figure 4.

Cytokine response modules at the site of disease in COVID-19

(A) Gene set enrichment analysis (GSEA) of the IL-1β and IL-6 modules was applied to nasopharyngeal swabs from SARS-CoV-2-infected and uninfected individuals. Patients were stratified into low (pink), medium (orange), and high (red) viral loads as previously described (Ramlall et al., 2020). GSEA was used to determine the level of engagement for the respective modules in the context of SARS-CoV-2 infection (Subramanian et al., 2005), in line with previously published analysis of this dataset (Ramlall et al., 2020). Normalized enrichment scores (NES) are shown on the x axes, and measurement of statistical significance (false detection rate q-value) is shown on the y axes. The threshold for significance (q = 0.05) is shown by the dotted lines; data points below the dotted lines are significantly enriched for the relevant module in each group of SARS-CoV-2 positive patients, in comparison to the control group.

(B) Leading edge enrichment plots from GSEA of the cytokine modules for each comparison.