Fig. 4

Differential expression between transition and normal appearing lung parenchyma regions (A) and dense fibrosis and normal appearing lung parenchyma (B) in IPF subjects adjusting for batch and estimated cell proportions of AEC1, AEC2, fibroblasts and ciliated cells. Venn diagram showing the overlap in DEGs between comparisons with normal lung parenchyma (C). Ingenuity canonical pathway (D) and upstream regulator analysis (E) of DEGs.  The activation z-score is a statistical measure based on the directional relationships between genes and their biological function. Orange indicates increased predictions over that of the null (positive z score), blue indicates decreased predictions (negative z score) and white z score of zero. Dots indicate that z score did not reach significance (1.645). Histology image showing changes in MUC5B and ATF4 (F). Immunofluorescence changes in MUC5B, ATF4 and ATF4 in KRT8 + cells between IPF and control in normal parenchyma regions (G). FOVs were chosen based on presence of features of interest (e.g. parenchyma, bronchiolar, etc.) in each section and 9 20x images centered randomly within the feature of interest were assembled into a composite. Pairwise comparisons are Mann-Whitney U test with significance set to (*) p < 0.05, (**) p < 0.01, (***) p < 0.001, (****) p < 0.0001