SAGE and quantitative PCR (qRT-PCR) analysis of select genes: (A) Genes found to have reversible expression upon smoking cessation. Box plots of SAGE data and histograms for qRT-PCR for CABYR, ENTPD8 and TFF3. Distribution of ratios between both current vs. former and current vs. former and never (Additional file IV) were found to be statistically different. (B) Genes found to be either partially or fully irreversible. Box plots of SAGE data and histograms for qRT-PCR for MUC5AC and GSK3B. Distribution of ratios between current vs. former and former vs. never were statistically different for MUC5AC and in addition, GSK3B was statistically significant for the combination of current and former vs. never. Box plot analysis was done using the Statistics toolbox from the MathWorks MatLab program. Red lines in the boxes represent the median expression value in terms of tags per million (TPM), and red "plus" signs represent outliers (values which are greater than 1.5 times the maximum value). The bottom and top part of the boxes represent the 2nd and 3rd quartiles of the data respectively. The error bars represent the 5th and 95th percentiles of the data. Quantitative RT-PCR validation was performed on a second cohort of nine current smokers, seven former smokers and six never smokers. Plotted is the average expression ratio relative to the average expression in never smokers of current (red), former (blue) and never (green) smokers. Statistical significance was determined using a one-tailed p-value from the Mann Whitney U Test (Supplemental Table IX).