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. 2021 Dec 2;12:7035. doi: 10.1038/s41467-021-27204-9

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — On the genome-wide scale, we explored the cis-effects of RNA editing events on their (a) gene expression, (b) transcript expression, and (c) protein expression. The volcano plots are shown on the left panels, and each dot represents one pair of one RNA editing event (orange for non-coding and blue for re-coding event) and its nearby gene. The X axis presents the regression coefficient (BETA) of the exposure variable of RNA editing binary status (0 for no RNA editing and 1 for having RNA editing), and the Y axis presents the −log10 transformed P values from the generalized linear regression model the fixed covariates of age at death, sex, postmortem interval, and RIN score. The displayed P values were not adjusted for the testing of multiple hypotheses and were derived by two-sided tests. The middle panels show the density plots and counts table to summarize the results shown in the volcano plot. The density plots show the comparisons of the association P values (−log10) of the non-coding (orange) and re-coding events (blue). The right panels showed the pie charts of the effects of non-coding events located in different genomic regions of 5′UTR (upper left), exons (upper right), 3′UTR (lower left) and introns (lower right). The positive effects are shown in a grade from pink (non-significance, P > 0.05) to brown (nominal-significance, Bonferroni-corrected genome-wide significance < P ≤ 0.05) to red (genome-wide significance, P ≤ Bonferroni-corrected genome-wide significance) while the negative effects are shown in a grade from light green (non-significance, P > 0.05) to green (nominal-significance, Bonferroni-corrected genome-wide significance < P ≤ 0.05) to dark green (non-significance, P > 0.05). d Results of a search for non-previously reported peptides based on the observed re-coding RNA editing events in the same subjects in ROSMAP (left) and different subjects in BANNER (right). The left nested pie charts show the matches of RNA re-coding events on the level of transcript (upper panel) and peptide (lower panel). On the right, based on the called 68 RNA re-coding events from unpaired ROSMAP DLPFC samples, five unique peptide sequences exist in an independent dataset with peptide spectrum matches >1.