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[Preprint]. 2024 May 31:2024.05.28.596138. [Version 1] doi: 10.1101/2024.05.28.596138

Figure 1: ProCapNet accurately predicts initiation rates and TSS positioning at base-pair resolution.

Figure 1:

(A) Design of ProCapNet, which is trained to predict base-resolution initiation events measured by PRO-cap. (B) Measured data, ProCapNet predictions, and ProCapNet contribution scores (for the profile and counts tasks) for two example PRO-cap peaks. Names of motifs highlighted by contribution scores are annotated. (C) Counts task performance on PRO-cap peaks from held out test chromosomes across 7-fold cross-validation. r, Pearson correlation. (D) Profile task performance on PRO-cap peaks from held out test chromosomes across 7-fold cross validation (higher JSD is worse). The y-axis shows the cumulative fraction of test peaks. (E) Profile task performance on held-out test peaks, stratified by overlap with ENCODE-annotated cis-regulatory elements. White dots are medians; the dashed line is the median for all test peaks. w/, with; w/o, without; Prox., proximal. JSD is normalized per-example to reduce confounding by coverage (see Methods; higher normalized JSD is worse).