Additional file 6 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

Additional file 6: Supplemental Table 3. Summary of the differential analysis of the TE families between the IPF patients and the donors in AT2 cells based on genomics regions and SQuIRE and REdiscoverTE analysis. A. Differential TE expression in exonic region in AT2 cells – RediscoverTE. B. Differential TE expression in intronic region in AT2 cells – RediscoverTE. C. Differential TE expression in intergenic region in AT2 cells– RediscoverTE. D. Summary of all changes obtained by SQuIRE and REdiscoverTE. E. Differential TE expression in intergenic region in AT2 cells- SQuIRE. Only significant TE families are shown. The columns represent the repeat classification, TE expression base mean (baseMean), log2 fold change (log2FoldChange), lfcSE (log fold standard error), stat (Wald statistics; lfc/standard error), p-value, p.adj (BH adjusted p-value).