Fig. 5

Abnormal mRNA processing in E16 livers. a Volcano plot of exon exclusion or inclusion events in RNA-seq data, from Additional file 5. Each dot represents a single exon. They are distributed across the x-axis according to a value between 0 and + 1 or -1 calculated for each exon as a measure of its mean exclusion or inclusion frequency in E16 compared to WT livers, and across the y-axis according to the p value for the difference between mean usage by E16 vs. WT livers, calculated by Welch's t-test. Dots stacked at the right edge represent exons skipped in E16 to some extent, but not at all in WT; dots at the left edge represent exons included in E16, but not in WT. The grey dashed line marks the p = 0.05 level. Many dots accumulate below this line, near the axis origins, indicative of abnormal exon usage both quantitatively small and also inconsistent. The 571 dots above the dashed line identify significant (p < 0.05) events of abnormal exon usage (206 inclusion, 365 exclusion) in mRNA from E16 livers. b Volcano plot of polyadenylation site (PAS) usage in RNA-seq data from Additional file 6. Each dot represents a single potential PAS. Values are represented as in panel a. The 3088 dots above the dashed line identify significant (p < 0.05) events (1607 effective PAS usage, 1481 transcription readthrough). c Correlation between abnormal exon usage and base composition biases in E16 livers. Each dot represents a single 5-mer motif; they are distributed across the x-axis according to their frequency of occurrence upstream (left), inside (middle), or downstream (right) exon boundaries, and across the y-axis based on their Spearman correlation with corresponding exon usage. Positive correlation indicates increased exon exclusion in the E16 mutant, relative to WT, whereas negative correlation indicates increased exon inclusion. Motifs showing significant correlation (n = 571, ρ > 0.0655 for positive correlation, ρ < − 0.0655 for negative correlation) are highlighted in red. Sequences of example motifs with statistically significant correlation and frequent occurrence are indicated