Fig. 5: BAL gene expression.

a, DEGs were identified using a four-way analysis of variance-like analysis with negative binomial generalized linear models. Mean normalized expression levels for significant genes are displayed for the four BAL clusters. b, Individual DEGs were identified across the four clusters (edgeR R package); variance-stabilized transformed gene counts for select genes highest in each of the four clusters were plotted (n = 127, 74, 45 and 32 for clusters 1–4, respectively). For all box plots: boxes indicate the median and IQR; the whiskers extend to the largest value above the 75th percentile (or smallest value below the 25th percentile), that is, within 1.5 times the IQR. c, Gene set enrichment scores to REACTOME pathways were calculated and example gene sets most enriched in each of the four clusters are shown.