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Fig. 2 | Genome Biology

Fig. 2

From: QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data

Fig. 2

3′ UTRs lengthen during neuronal differentiation. a Scatterplot comparing the projections of QAPA PPAU profiles onto first (x-axis) and second (y-axis) principal components. Each point indicates the median values for a DIV stage over replicates. Mature neurons appear at DIV ≥ 7. Note that PC1 sorts samples by increasing development time as indicated above the plot. b Lines show the median PPAU (y-axis) of the top 100 3′ UTRs with largest absolute principal component loadings for PC1 (purple) and PC2 (orange) across increasing development time (x-axis). c Bar plot indicates the number of 3′ UTRs that lengthen (∆PPAU > 20), shorten (∆PPAU < −20), and do not change (|∆PPAU| ≤ 20) where ∆PPAU is defined as the difference in PPAU between ESC stages (DIV ≤ −4) and mature neuron stages (DIV ≥ 7). d Heat map displays PPAUs across DIV stages for the 608 genes whose |∆PPAU| > 20. Columns correspond to genes and are sorted to be consistent with the hierarchical clustering dendrogram shown above the heatmap. Rows correspond to DIV stages. To emphasize 3′ UTR lengthening, the distal PAU (= 100 − PPAU) is shown. e Combined violin and box plots comparing the lengths of the extended, alternative 3′ UTR (aUTR) regions in lengthening, shortening, and non-changing 3′ UTRs. P values were computed using Kolmogorov–Smirnov test. f Enrichment map summarizing gene set enrichment analysis results of Gene Ontology (GO) terms enriched in the genes with 3′ UTR lengthening. Nodes represent a GO term and links between two nodes indicate that more than 90% of the genes in the smaller term are also in the larger term

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