Additional file 7 of The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis

Additional file 7: Supplemental Table 4. Summary of the differential analysis and correlation between the L1HS and their functionally related genes in AT2 cells. A. Manually curated list of genes known to be part of the L1HS defense and antiviral interferon-stimulating genes [25, 39]. B. List of all significant differentially expressed genes in AT2 cells, with functional annotation of L1HS related genes. Only significant genes are shown. The columns represent the gene names, gene 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). C. Summary of the linear model test of association between the expression of L1HS -related genes and L1HS. The p value1 represents relationship between gene expression and L1HS-locus expression, and the p value2 - represent difference in the regression slopes between the two groups (IPF and donor). The p-value correction was performed using the Benjamini and Hochberg (BH) test and (p.adjust1 and p.adjust2). Model: Gene expression∼L1HS expression + group (IPF/Donor).