Fig. 5
Downregulated TEs are associated with LSD1 occupancy and transcriptional repression in SCLC. A Boxplot of LSD1 gene expression in 24 tumour and matched normal samples expressed as log2(normalized counts expression + 1). Paired t-test p-values are reported. B Mean of Normalized read levels for H3K4me2 over downregulated ERV genomic loci (purple) in H526 SCLC cell line and mean genomic signal of ChIP/input ratio over same loci for LSD1 in H526 SCLC cell line in untreated (blue) and treated with LSD1 inhibitor (green) conditions. C Ridgeline plot showing the distribution of relative ranking metric values expressed as Wald test statistic values from GSEA (x-axis) of genes proximal to downregulated TEs (y-axis) in SCLCs. Colour: GSEA p-values, as in legend. For each TE, the ratio between the number of loci located upstream control regions of genes over the total number of loci is reported. D GSEA plot of genes, in the upstream regulatory regions of which LTR30 elements are localized (n = 4). Top: position of genes along the ranked list of genes with relative ranking metric values expressed as Wald test statistic values. Bottom: running enrichment score line plot; vertical red line indicates the peak of the plot at which the ES is computed. Normalized enrichment score (NES) and adjusted p-values are indicated