Figure 2.

Intron retention might increase intronic TE measurements. (A) Distribution of the mean expression of TEs located in retained introns (light grey) compared to the mean expression of TEs located in randomly chosen introns (dark grey). p-value is reported on the top of the plot. (B) Pie chart reporting the percentage of positive, negative, and non-significant correlations between TE expression and the hosting intron’s IRratio. (C) Distribution of significant (adjusted p-value < 0.05) coefficients of correlation between TE expression and hosting intron’s IRratio. (D) Comparison between the number of commonly retained introns containing at least one transcribed TE (red dashed line) in the Geuvadis dataset with the mean of 1000 randomizations of randomly chosen introns (light grey distribution). Z-score is reported on the top of the plot. E Comparison between the number of commonly retained introns containing at least one TE fragment (red dashed line) in the Geuvadis dataset compared to the mean of 1000 randomizations of randomly chosen introns (light grey distribution). Z-score is reported on the top of the plot.