Additional file 5 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

Additional file 5: Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis. A. Whole-lung (WL) tissue - SQuIRE, B. Alveolar type II (AT2) cells - SQuIRE. C. Alveolar macrophages (AM) - SQuIRE. D. Whole-lung (WL) tissue - REdiscoverTE, E. Alveolar type II (AT2) cells - REdiscoverTE. F. Alveolar macrophages (AM) - REdiscoverTE. The columns represent the repeat classification, the 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). Only significant upregulated families are shown. G. Summary of all changes in REdiscoverTE analysis.

附加文件5：补充表2。本表格汇总了基于SQuIRE与REdiscoverTE两种分析工具，对不同细胞类型中特发性肺纤维化（Idiopathic Pulmonary Fibrosis, IPF）患者与健康供体的转座因子（Transposable Element, TE）家族的差异分析结果。
A. 全肺组织（Whole-lung, WL）——SQuIRE分析；
B. 肺泡II型细胞（Alveolar type II, AT2）——SQuIRE分析；
C. 肺泡巨噬细胞（Alveolar macrophages, AM）——SQuIRE分析；
D. 全肺组织（WL）——REdiscoverTE分析；
E. 肺泡II型细胞（AT2）——REdiscoverTE分析；
F. 肺泡巨噬细胞（AM）——REdiscoverTE分析。
表格各列依次对应：重复序列分类、TE表达基础均值（baseMean）、log2倍变化（log2FoldChange）、log2倍变化标准误（lfcSE）、Wald检验统计量（stat，即log2倍变化值与标准误的比值）、p值（p-value）、经Benjamini-Hochberg（BH）法校正的p值（p.adj）。本部分仅展示显著上调的TE家族。
G. REdiscoverTE分析中所有差异变化情况的汇总。