Fig. 1
From: Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
Schematic outline of the KAPAC approach. a Tabulation of the relative usage of poly(A) sites in different experimental conditions (here, control and treatment). b Tabulation of k-mer counts for regions (blue) located at a defined distance with respect to poly(A) sites p. c Based on the usage of poly(A) sites relative to the mean across samples and the counts of k-mers k in windows located at specific distances from the poly(A) sites p, KAPAC infers activities Ak,s of k-mers in samples s. cs,e is the mean relative usage of poly(A) sites from exon e in sample s, c p is the mean log2-relative usage of poly(A) site p across samples, and ε is the residual error. KAPAC ranks k-mers based on the absolute z-score of the mean activity difference in two conditions (here, in control relative to treatment). d Fitting the KAPAC model for windows located at specific distances relative to poly(A) sites, position-dependent activities of sequence motifs on poly(A) site use are inferred