Fig. 1
TEs are deregulated in human SCLCs. A Design of data analyses performed starting from collecting RNA-seq data from three public datasets of SCLC samples. Intergenic transposable element expression was quantified with RediscoverTE [14] and differential expression analysis was performed. Then we characterized deregulated TEs involvement in innate immune induction, epigenetic changes in SCLC and patient survival. Created with BioRender.com. B PCA plot of SCLC sample datasets based on transposable element expression. Samples are 104 SCLC from three different EGA Datasets (magenta circles, triangles and squares) and 24 normal lung (green circles) samples. C Volcano plot of differentially expressed intergenic TEs in 24 SCLC vs matched normal samples. X-axis: log2 fold change values of differential expression. Y axis: -Log10(q-value). Points correspond to intergenic TE copies included in DNA, LTR, LINE, SINE, Penelope and retroposons classes (n = 1040). Labels are assigned only to intergenic differentially expressed TEs (n = 52). Red points correspond to differentially expressed TEs with log2 fold change ≥ + 1 or log2 fold change ≤ − 1 and q-value ≤0.05. Yellow points correspond to differentially expressed TEs with log2 fold change ≥ + 1 or log2 fold change ≤ − 1 and q-value ≥0.05. D Stacked bar plot of the number of upregulated (left) and downregulated (right) transposable element copies summarized for each family and grouped for each class in SCLC tumour vs matched normal samples. Gradient colour is shown according to the legend