Figure 2.

Composition of the healthy nonsmoker small airway epithelium (SAE) transcriptome. A. Comparison of the SAE transcriptome to that of other tissues. Abscissa - the number of genes, with the genes in descending order of mRNA level. Ordinate - fraction of all mRNAs derived from these genes. The genes expressed by the small airway epithelium (blue) are compared to genes expressed by other organs as indicated [24]. Note that the SAE is similar to liver in that a few genes are expressed at very high levels. B. RNA-Seq sequence alignments for SCGB1A1 (uteroglobin; CC10), the most highly expressed gene in the SAE. The region of the genome corresponding to SCGB1A1 is shown with the read coverage depth for 5 healthy nonsmokers plotted using Partek Genomics Suite version 6.5. RPKM for whole mRNA for each subject is shown on the left. C-E. Frequency distribution of expression level for ubiquitous vs SAE-enriched genes in the small airway epithelium of healthy nonsmokers. "Ubiquitous" genes are those expressed by most tissues; "SAE-enriched" genes are those more abundant in SAE compared to other tissues (see text). For all panels, the number of genes in 1/2 log₁₀ bins was determined starting at the detection limit (RPKM = 0.125). For each panel, the expressed genes are grouped (in 1/2 log₁₀ bins); low (-0.9 to 1), median (> 1 to 10) and high (> 10), with the number of genes and % in each category listed and median RPKM for n = 5 healthy nonsmokers. C. All genes. D. Ubiquitous genes, representing 48% of all expressed genes. E. SAE-enriched genes representing 52% of all expressed genes. Note that the SAE-enriched genes have a much larger proportion of low level expressed genes compared to the ubiquitous genes. F, G. Comparison of coverage of RNA-Seq and microarray assessment of SAE gene expression of healthy nonsmokers. Genes assessed by RNA-Seq were divided into low (0.125-1), median (> 1-10) and high (> 10) RPKM on the basis of median expression level in n = 5 nonsmokers. Affymetrix U133 data for small airway epithelium for n = 27 African-American healthy nonsmokers [[129]; Additional file 1, Table S1] were assessed based on the Affymetrix P calls in low expression (Affymetrix "present (P)" in < 50%; red) or high expression in microarray ("P" in > 50%; blue). Genes with no unique probe on the microarray are identified in green. F. Ubiquitous genes. G. SAE- enriched genes. For medium and high expressing genes the microarray and RNA-Seq are very similar in detecting expressed genes, but for the SAE-enriched, low level expressed genes detected by RNA-Seq, the microarrays miss a large proportion of the genes.