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. 2022 May 27;11(6):826. doi: 10.3390/biology11060826

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© 2022 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Differential intron retention between groups biases a correct TEs differential expression analysis. (A) Volcano plot reporting the number of deregulated introns in IR-High vs. IR-Low samples from Geuvadis dataset. Significant results are reported in dark grey (B) Volcano plot reporting the number of deregulated TEs in IR-High vs. IR-Low samples from Geuvadis dataset. Significant results are reported in dark grey. (C) Genomic distribution of upregulated TEs (light grey) in IR-High with respect to IR-Low samples compared to the mean of 1000 randomizations (dark grey). Z-score are reported as numbers on the top of the plot. Error bars represent the standard deviation. (D) Volcano plot reporting the number of deregulated introns in DNMT^-/- samples vs. WT control. Significant results are reported in dark grey. (E) Volcano plot reporting the number of deregulated TEs in DNMT^-/- samples vs. WT control. Significant results are reported in dark grey. (F) Genomic distribution of upregulated TEs (light grey) in DNMT^-/- samples, with respect to WT controls, compared to the mean of 1000 randomizations (dark grey). Z-scores are reported as numbers on the top of the plot. Error bars represent the standard deviation. (G) Volcano plot reporting the number of deregulated introns in SDE2 knock-down cells with respect to control cells. Significant results are reported in dark grey. (H) Volcano plot reporting the number of deregulated TEs in SDE2 knock-down cells with respect to controls samples. Significant results are reported in dark grey. (I) Genomic distribution of upregulated TEs (light grey) in SDE2 knock-down cells compared to the mean of 1000 randomizations (dark grey). Z-scores are reported as numbers on the top of the plot. Error bars represent the standard deviation.