Fig. 2

Enrichment of transcription factor motifs in differential accessible regions. a-d Scatter plot shows the enrichment of predicted Transcription Factor (TF) motifs (from JASPAR) in gained and lost peaks of breast and colon cancers. Each dot represents a TF, the y-axis represents the proportion of peaks overlapped with the predicted motifs of that particular TF, and the x-axis represents the significance of enrichment compared to random peaks computed using one-sided Fisher’s exact test. The TFs that were significantly enriched (q-value <=0.1) are highlighted in black. Sequence logo of a few significant TF motifs is shown beside the scatter plots. e, f The panels show the logo of de novo sequence motifs identified by HOMER in the group A and B peaks (see methods) and their similarity with the known TF motifs (the value close to 1 indicates high similarity). The donut plot besides it shows the distribution of genomic features in peaks that contained the particular motif. The colour code corresponds to the genomic features shown in Fig. 1a-b. g-l The plot shows the accessibility score at the centre of peaks (containing specific TF motif) compared to its immediate flanking regions in mutant and wild-type p53 samples. The colour of the line indicates different mutant samples and the text colour of the motif name represents whether it was found from JASPAR or HOMER de novo motif analysis