Fig. 5

Inferring 3′ aQTL effect sizes from sequence. A Total number of 3′ aQTLs, cis-acting aQTLs, and lead aQTLs respectively (GTEx v7). Right: Predicted vs measured aQTL effect sizes in the lung. B Predicted vs measured 3′ aQTL effect size Spearman r’s (GTEx v7). Each dot corresponds to the correlation in a particular tissue type. C Predicted vs measured aQTL effect sizes of the data from Mittleman et al. [21] (\(n = 58\)). D Multiple softmax regression for predicting tissue-specific isoform abundance. APARENT2 (green) and the tissue model (blue) are used to score each PAS. E Increase (red) or decrease (blue) in Spearman r when using a particular tissue model to scale the 3′ aQTL predictions made by APARENT2 in a given GTEx tissue (testis, ovary, B-cell lymphocytes, and brain). F Reconstructive mask for a SNP in the ALDH7A1 gene, with a brain-specific effect. The bottom mask is the result of 64 randomly initialized optimization attempts. Boxplot shows differential PAS usage in data from Lianoglou et al. [42]