Additional file 10 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

Additional file 10: Supplemental Table 7. Summary of the differential analysis of the genes and TEs per individual cell type in the scRNA-seq. Table 5A. Cell number for each subject in each cell type. B. Differentially expressed genes in IPF vs Donor for all cell types. Avg_logFC: Average log fold change; p-value: calculated based on the Wilcoxon rank-sum test; p.adjust: adjusted p-value based on the Bonferroni correction using all the genes in the dataset; pct.1: fraction of the cells that express the gene in IPF patients; pct.2: fraction of the cells that express the gene in donors. C. Differentially expressed TE families in the IPF patient vs. donor samples for the different cell types. D. Differences between the IPF patients and donors represented as correlation between L1 score and TE-related gene expression. A subset of 126 genes identified in RNA bulk seq were tested. A linear model was fitted for each L1 score and the gene pairs. The p-value was calculated using t-test; p.adjust is the Benjamini and Hochberg (BH)-adjusted p-value.