Comparison of males and females with COPD using a standard differential-expression analysis approach. (A) A PCA analysis on expression data using genes located on the Y chromosome. Males and females cluster into two groups. (B) Covariate information for the 42 female and 84 male subjects included in the analysis. The statistical difference between sexes for age and pack-years was calculated using an unpaired two-sample t-test and the statistical difference between the sexes for GOLD stage was calculated by applying a chi-squared test to a two by three (sex by stage) contingency table. (C) The top most differentially-expressed genes based on a using an unpaired two-tailed t-test (after specifically excluding genes those on the sex chromosomes). Genes with higher average expression in female are colored pink and those with higher average expression in male are colored blue. (D) The results of a GSEA analysis looking for GO category differential-expression between males and females. The five most differentially-expressed GO categories in males and females in either sputum or blood are shown. Deeper shades of pink are used to denote greater significance in female while deeper shades of blue indicate greater significance in males. The scale is based on the –log FDR significance for categories enriched in females, resulting in positive values, and on the + log FDR significance for categories enriched in males, resulting in negative values. Note that the color-range extends to an FDR significance of 10−3 in each sex even though the most significant categories found in this analysis only reach an FDR significance of around 10−2. (E) GSEA “enrichment plots” for the two most significantly differentially-expressed GO categories according to the GSEA analysis in males and females in either sputum or blood.