After trying to change the plotgroups variable in the Differential Expression section 4 above to one of the other pairwise comparisons, also run through the Functional Annotation analysis for this second comparison.
For example, compare Basal_cells to Murine_tracheal_epithelial_cell for the functional annotation analysis.
How does the KEGG pathway and GO term enrichments vary between the two comparisons you’ve just done (i.e. the Basal_cells to Differentiated_cells vs Basal_cells to Murine_tracheal_epithelial_cell comparison)?