Extended Data Fig. 3: BPNet and TF-MoDISco outperform traditional methods in motif discovery and the mapping of motif instances.

a, Motifs discovered by ChExMix, HOMER and MEME for Oct4, Sox2, Nanog and Klf4 ChIP-nexus peaks that are closest to the 11 primary representative BPNet motifs (top row). Green checkmark denotes whether the discovered motif is similar to the BPNet motif. b, Number of motif instances located up to 500 bp (top) or 100 bp (bottom) away from the ChIP-nexus peak summits showing a strong ChIP-nexus footprint. Only motif instances in peaks from held-out test chromosomes (1, 8 and 9) were used for the evaluation. (x-axis) top N motif instances from each of the methods were sorted in descending order of scores (PWM log odds score or CWM contrib score). For BPNet-augm, the center of the genomic region for which the contribution scores were computed was randomly jittered up to 200 bp away from the peak summit. This augmentation prevents BPNet from using the positional information of the peak summit. In the final column (Nanog replicate), the Nanog ChIP-nexus footprint was measured by a separate biological replicate using a different antibody (ɑ-Nanog from Abcam, ab214549), which was not used during training or evaluation.