A description of the transcriptome of human bronchial epithelium should provide a 
basis for studying lung diseases including cancer. We have deduced global gene 
expression profiles of bronchial epithelium and lung parenchyma, based upon a vast 
data set of nearly two million sequence tags from 21 serial analysis of gene 
expression (SAGE) libraries from individuals with a history of smoking. Our 
analysis suggests that the transcriptome of the bronchial epithelium is distinct 
from that of lung parenchyma and other tissue types. Moreover, our analysis has 
identified novel bronchial-enriched genes such as MS4A8B, and has demonstrated the 
utility of SAGE for the discovery of novel transcript variants. Significantly, 
gene expression associated with ciliogenesis is evident in bronchial epithelium, 
and includes the expression of transcripts specifying axonemal proteins DNAI2, 
SPAG6, ASP, and FOXJ1 transcription factor. Moreover, expression of potential 
regulators of ciliogenesis such as MDAC1, NYD-SP29, ARMC3 and ARMC4 were also 
identified. This study represents a comprehensive delineation of the bronchial 
and parenchyma transcriptomes, identifying more than 20,000 known and hypothetical 
genes expressed in the human lung, and constitutes one of the largest human SAGE 
studies reported to date.