Supplementary Figure 2: Two core exacerbation modules are downregulated in cold events that lead to exacerbation.

(a) The expression levels of the 2 nasal gene expression modules that decreased in Ex+ events compared to Ex- events. FDR values from top to bottom are 1.38E-05, 4.09E-04. Expression levels represent the log base 2 of the geometric mean of the normalized expression of all genes within the module. Shown are group mean values, interquartile ranges, and all data points. Sample sizes are: Ex+ at baseline (n = 38); Ex+ at 0–3 days (n = 44); Ex+ at 4–6 days (n = 11); Ex- at baseline (n = 68); Ex- at 0–3 days (n = 97); Ex- at 4–6 days (n = 95). 18 participants who had one Ex+ and one Ex- event have the same measurement shown in both Ex+ at baseline and Ex- at baseline. All measurements shown are otherwise biologically independent. Comparisons were performed using a weighted linear model and empirical Bayes method, including terms for exacerbation status, cell percentages, presence or absence of virus, visit, and library depth with a random effect included for participant. (b) Gene-gene association networks for each of the modules demonstrate significant interaction networks. Genes are represented as circular nodes, and known gene-gene interactions from STRING as connecting edges. The size of each node is proportional to the number of interactions. STRING enrichment p-values for both networks are <1.0E-16.