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. 2021 Sep 20;10:e69148. doi: 10.7554/eLife.69148

Figure 3. Characterization of cis- and trans-regulatory features of conserved circular RNAs (circRNAs).

(A) Barplot describing feature importance for logistic regression model of conserved circRNAs compared to background. Colors represent positive or negative influence. Transparency reflects log10(p-value of z-statistic). Error bars represent standard error. ‘_1’ is relative to first exon of circRNA and ‘_2’ is relative to final exon of circRNA. ss3: 3´-splice site; ss5: 5´-splice site; Alt3ss: alternative 3´-splice sites. Inverted repeats are repetitive elements on opposite strands in introns adjacent to circRNAs. See Supplementary file 3 for details of features. (B) Barplot describing feature importance for logistic regression model of conserved circRNAs compared to species-specific circRNAs. See (A) for plot interpretation and descriptions. (C) Cumulative distribution plots describing (left; p<1.39 × 10–09) 5´-splice site strength at final exon of circRNAs and (right; p<1.37 × 10–05) distribution of nucleosomes on intron downstream of circRNA. p-Values calculated by Wilcoxon rank-sum test and corrected for multitesting (Bonferroni). See Figure 2D for interpretation of cumulative distribution plot. (D) Pyramid plot showing the mean fraction of circRNAs with selected inverted repeat retrotransposon elements in adjacent introns.

Figure 3.

Figure 3—figure supplement 1. Performance assessment of logistic regression model.

Figure 3—figure supplement 1.

(A) A receiving operating characteristic curve (ROC) plot displaying the sensitivity (true-positive rate) compared to the selectivity (false-positive rate) for the logistic regression model (conserved vs. background circular RNA [circRNA]). (B) An ROC plot for logistic regression model (conserved vs. species-specific circRNA). (C) Cumulative distribution plots comparing conserved versus background circRNAs of (left) alternative 3´-splice sites (ss) within first exon of the circRNA and (right) of serine/arginine (SR) RNA-binding peaks from CLiP data. p-Values calculated by Wilcoxon rank-sum test and corrected for multitesting (Bonferroni) (see Figure 2D for description of cumulative distribution plots). (D) Cumulative distribution plots comparing conserved versus species-specific circRNAs of (left) nucleosome peaks in downstream intron adjacent to circRNA and (right) of Alu element content in upstream intron adjacent to circRNA (see Figure 2D for description of cumulative distribution plots). p-Values calculated by Wilcoxon rank-sum test and corrected for multitesting (Bonferroni).