Fig. 3.
From: MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads
Differential APA analysis by MAAPER using QuantSeq FWD data. A Schematic illustrating the calculation of relative expression difference (RED) and relative length difference (RLD) scores. REDu and RLDu are for 3′UTR APA, whereas REDi and RLDi are for intronic APA. ORF, open reading frame. B Distribution of -log10(FDR-adjusted P) in differential APA analysis. The plotted data are based on the average across all samples. The adjusted P = 0.01 was used as a threshold to identify significant APA events. C Distributions of REDu (left) and RLDu (right) scores calculated for AS, RC4, and RC8 samples compared with NT. Only genes that showed significant APA changes in at least one sample were included. D Read coverage and PAS prediction results for the gene Nmt1. E Distributions of REDi (left) and RLDi (right) scores calculated for AS, RC4, and RC8 samples compared with NT. Only genes that showed significant APA changes in at least one sample were included. F Read coverage and PAS prediction results for the gene Zfp444