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Fig. 2 | Mobile DNA

Fig. 2

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

Fig. 2

L1HS 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 expressionL1HS 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-C

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