Fig. 2From: The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosisL1HS intergenic expression is associated with the IPF phenotype and expression of genes with functional relevance to L1HS activity in AT2 cells. a L1HS intergenic expression in Donor and IPF samples as quantified by REdiscoverTE method. Green: donor samples. Red: IPF samples. The x-axis represents groups; the y-axis represents log-normalized L1HS expression values. L1HS expression between the groups is significantly different as determined by DESeq2 analysis (p.adjust = 0.001). b Heatmap of differentially expressed genes from four gene sets which are functionally relevant to L1HS activity [28, 29]: type I interferons (IFN-I, 33 out of 84 genes), senescence-associated secretory phenotype genes (SASP, 34 out of 85 genes), L1 transcriptional regulator genes (1 out of 2 genes), and L1 post-transcriptional regulator genes (6 out of 17 genes). The heatmap colors represent Z-score of log-normalized gene expression. The y-axis represents four gene sets. Samples are grouped on the x-axis by their phenotypes. c Examples of L1HS co-expression correlation with genes functionally relevant to L1HS activity from four gene sets: INF-I pathway (DDX58, IFI16, STAT1, IRF9, ISG15), senescence-associated secretory phenotype (SASP) genes (MMP3, SERPINE 1), L1 transcriptional regulator genes (FOXA1), and L1 post-transcriptional regulator genes (SAMHD1, MOV10, and APOBEC3G, CALCOCO2). Plots show the linear relationship of log-normalized gene expression which represents dependent variable (y-axis), and L1HS as an independent variable (x-axis) in the AT2 cells. Phenotype group (IPF/donor) was included as a covariate in the model. (Model: Gene expression∼L1HS expression + group (IPF/Donor). The colors represent the phenotypes (Green: donor; Red: IPF), and the gray line is the best fit from linear model. The R2 values from linear model fit of each gene-L1HS relationship are shown. The BH p-adjusted values (p) < 0.05) for each relationship are shown; p represents relationship between gene expression and L1HS expression. Results of all tested genes are summarized in Supplemental Table 4B-CBack to article page