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).

附加文件6：补充表3。基于基因组区域，结合SQuIRE与REdiscoverTE分析，针对AT2细胞中特发性肺纤维化（IPF）患者与供体的转座子（Transposable Element，TE）家族差异分析总结。A. AT2细胞外显子区域转座子差异表达分析——RediscoverTE；B. AT2细胞内含子区域转座子差异表达分析——RediscoverTE；C. AT2细胞基因间区域转座子差异表达分析——RediscoverTE；D. SQuIRE与REdiscoverTE分析所得全部变化结果汇总；E. AT2细胞基因间区域转座子差异表达分析——SQuIRE，仅展示具有统计学显著性的转座子家族。各列依次代表重复序列分类、转座子表达基准均值（baseMean）、对数2倍变化值（log2FoldChange）、对数2倍变化标准误（lfcSE，log fold standard error）、检验统计量（Wald统计量，即log2倍变化与标准误的比值，stat）、原始P值、BH校正后P值（p.adj，BH adjusted p-value）。