Fig. 4

Gene expression profiles of uninvolved regions in IPF and CHP, and central regions in normal cases. (a) PCA plot of ROIs, grouped by condition. (b) Two clusters of top differentially expressed genes (sorted by F statistic) between uninvolved regions in IPF and CHP, and central regions in normal controls. Expression is shown as row-scaled Z scores. Each column represents a unique ROI that belongs to indicated annotation-subtype. A row dendrogram is shown on the left. (c) Top 5 overrepresented GO biological process pathways by significantly up or downregulated genes based on adjusted P value < 0.05 and absolute log2 fold change ≥ 1 in indicated comparisons. Dot size and color represent the number of genes in each pathway, and adjusted P value, respectively. (d) Volcano plots of differentially upregulated (red) or downregulated (blue) genes based on adjusted P value < 0.05 and absolute log2 fold change ≥ 1 for indicated pairwise comparisons between regions. (e) Venn diagrams of the number of up or downregulated genes in uninvolved regions of IPF or CHP compared to bona fide normal controls.