Extended Data Fig. 7: Helical periodicity of Nanog motifs is not discovered with traditional methods and requires BPNet’s large receptive field.
From: Base-resolution models of transcription-factor binding reveal soft motif syntax
a, The pairwise spacing of Nanog motif instances located up to 100 bp away from the ChIP-nexus peak summits in all possible strand orientations (rows) for different methods and/or thresholds (columns). Results for all chromosomes are shown. b, The pairwise spacing of Nanog motif instances when BPNet is trained with different numbers of convolutional layers (Fig. 1g). BPNet with only a single convolutional layer (first column) is unable to capture the 10 bp periodicity due to the limited receptive field similar to PWMs.
