Figure 6.

Overall impact of smoking on small airway epithelium gene expression. Shown are comparisons of RNA-Seq assessment of genes expressed in the small airway epithelium (SAE) in nonsmokers (n = 5) vs smokers (n = 6). A. Cumulative frequency of expression levels as a function of increasing RPKM. The data is shown as cumulative frequency in 1/2 log10 bins starting at the lower limit (RPKM 0.125, log10 = -0.9) for healthy nonsmokers (blue) and healthy smokers (red). On an overall basis assessing all genes, there is no difference in the nonsmokers vs smokers. B. Comparison of expression of the subset of smoking-responsive vs non-responsive genes for the ubiquitous and SAE-enriched genes. Each category is divided into low, medium and high expression groups using the same criteria as in Figures 2, 3, with smoking-responsive genes defined as p < 0.05. Ordinate - number of genes; abscissa - smoking responsive (red) and smoking non-responsive (blue) for ubiquitous and small airway epithelium (SAE)-enriched genes. Note that for both ubiquitous and SAE-enriched genes, only a small fraction, and approximately the same proportion (8-14%; low, medium, high), are smoking-responsive. C, D. Modified volcano plot showing absolute change in expression level (RPKM smoker - RPKM nonsmoker) vs -log p value for ubiquitous and SAE-enriched genes. C. Ubiquitous genes. D. SAE-enriched genes. Note that for both ubiquitous and SAE-enriched genes, more genes are down-regulated by smoking than up-regulated.

Hackett et al. BMC Genomics 2012 13:82   doi:10.1186/1471-2164-13-82
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