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Fig. 3 | Genome Biology

Fig. 3

From: MMSplice: modular modeling improves the predictions of genetic variant effects on splicing

Fig. 3

Evaluation of models predicting ΔΨ5 and ΔΨ3 on the GTEx dataset. Associated effects (y-axis) versus predictions (x-axis) for GTEx variants around alternative spliced donors (3 nt in the exon and 6 nt in the intron) and acceptors (3 nt in the exon and 20 nt in the intron) were considered. Ψ5 (or Ψ3) of homozygous (black) and heterozygous (blue) alternative variants as well as homozygous reference variants were calculated by taking the mean Ψ5 (or Ψ3) across individuals with the same genotype (excluding individuals with multiple variants within 300 nt around splice sites) on brain and skin (not sun exposed) samples. For donor variants, MMSplice (a) was benchmarked against COSSMO (b), HAL (c), and MaxEntScan (d). For acceptor variants, MMSplice (e) was benchmarked against COSSMO (f) and MaxEntScan (g). The 95% confidence intervals for Pearson correlation (R) and root-mean-square errors (RMSE) were calculated with bootstrap (“Methods” section). The dotted line marks the y=x diagonal

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