Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms
Fig 6
Evaluation of differential chemokine networks in IPF subsets.
A. Hierarchical clustering of GSE47460 (Kaminski-LGRC bulk expression cohort) [14–17] IPF patients based on chemokines differentially expressed between IPF subsets. Absolute log FC >0.58 and adjusted p value<0.05 was used to define differentially expressed chemokines. x axis represents individual patients, y axis represents genes. Subsets are indicated in x axis color bar and legend of heatmap and correspond to classes shown in Fig 1A. B. Expression of chemokines detectable in GSE135893 (Kropski-Vanderbilt Univ single cell cohort) [24] scRNAseq data and in GSE47460 (Kaminski-LGRC bulk expression cohort) [14–17] IPF subsets. scRNAseq UMAP plots (top row) were generated using the ‘FeaturePlot’ function in R package Seurat. Each UMAP plot depicts the expression of the chemokine indicated. Color bars indicate scaled expression in each cell on the plot. Cell clusters correspond to clusters reported in S5 Fig. Bar plots (bottom row) depict the expression of the same chemokines in GSE47460 (Kaminski-LGRC bulk expression cohort) [14–17] IPF subsets. Adjusted p values are reported on plots.