Fig. 2
From: Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
KAPAC accurately uncovers the activity of known regulators of poly(A) site choice. a Smoothened (± 5 nt) density of non-overlapping (C)3 motifs in the vicinity of poly(A) sites that are consistently processed (increased or decreased use) in two PCBP1 knock-down experiments from which 3′ end sequencing data are available [23]. Shaded areas indicate standard deviations based on binomial sampling. b Difference of (C)3 motif activity inferred by KAPAC in the two replicates of control (Ctrl) versus PCBP1 knock-down (KD) experiments (number of PAS n = 3737). The positive differences indicate that (C)3 motifs are associated with increased PAS use in control samples. The table shows the three most significant motifs, with the z-score and position of the window from which they were inferred. c Model of the KAPAC-inferred impact of PCBP1 on CPA. d Smoothened (± 5 nt) density of non-overlapping (U)5 tracts in the vicinity of sites that are consistently processed (increased or decreased use) in two HNRNPC knock-down experiments [29]. e Difference of (U)5 motif activity inferred by KAPAC in the two replicates of control (Ctrl) versus HNRNPC knock-down (KD) experiments (n = 4703). The negative differences indicate that (U)5 motifs are associated with decreased PAS use in the control samples. The table with the three most significant motifs is also shown, as in b. f Model of the KAPAC-inferred impact of HNRNPC on CPA