Fig. 4. Global binding and expression differences in wild-type and mutant U2AF1.

a U2AF1 S34F globally alters binding in HCC78. Scatter plots comparing CLIP reads of individual genes bound to wild-type and mutant U2AF1. Genes that were preferentially bound (fold change >1.5) in favor of mutant (red) and wild-type (blue) are shown. b U2AF1 S34F globally alters expression in HCC78. Scatter plots comparing FPKM values of individual genes bound to wild-type and mutant U2AF1. Genes that were preferentially expressed (fold change >1.5) in favor of mutant (red) and wild-type (blue) are shown. c Comparison of mutant to wild-type ratios U2AF1 CLIP reads and FPKM values of individual genes. 87 genes for mutant and 23 genes for wild-type are shown to be differentially bound and expressed in favor of the mutant and wild-type, respectively. d Cumulative frequencies of alternative splicing events. A statistically significant threshold for alternative splicing events comparing wild-type and mutant U2AF1 (Bayes factor >5) is shown. A3′SS, alternative 3′ SSs; A5’SS, alternative 5’ splice sites; SE, skipped exons; RI, retained introns. e Alternative splicing events preferentially spliced in favor of mutant or wild-type U2AF1 at greater than 10% frequency (Bayes factor >5). ∆PSI = difference in “percentage spliced in”. f Scatter plot comparison of expected alternative splicing events and observed events as a percentage of all events. Gray area represents statistically significant region with P < 0.01. g The frequency of each trinucleotide at 3′ splice sites of alternatively skipped exons in U2AF1 S34F mutant and wild-type transduced cells based on their change in inclusion. h Fraction of skipped exon events with TAG or CAG at the 3′ splice site in wild-type and U2AF1 S34F mutant TCGA LUAD cases (n = 175 for wild-type and 125 for mutant). i Overlap of differentially skipped exon events in HCC78 (Z-score of ψ greater/less than ±1.64, P = 0.05) and TCGA U2AF1 S34F mutant LUAD cases (P = 0.05).