Fig. 8
Differential L1 score distribution in the AT2 cells and its association with cellular factors. a The L1 score differences in the AT2 cells from eight fibrotic (red) vs. eight donor (green) lungs (p = 1.18-e09, n = 8 per phenotypic group). The L1 scores were calculated per each cell using all the expressed L1 elements, and the significance of the L1 score distribution between the phenotypes was determined using the Wilcoxon rank-sum test. The calculations were performed using the Seurat (v3) R package. b Correlation plot showing the relationship between the TE L1 score and the individual TE-related genes in the AT2 cells. The difference in the gene expression response to the L1 score in the AT2 cells was modeled using the lm function in R, the TE L1 score (independent variable), and the log2 transformed gene expression (dependent variable). To determine whether the relationship between L1 score and average gene expression differs between IPF and donors we used t-test. The p-value was corrected for multiple tests using the Benjamini and Hochberg (BH) test. Significant p-values (p.adjust < 0.05) are shown