Fig. 3: Modulation of the chromatin accessibility landscape and transcription factor binding motif enrichments following chemotherapy.

A Proportion of total stratified by chemotherapy. Points represent the within-sample cluster fraction and p value determined by Mann–Whitney test. B Summary counts of differentially accessible chromatin (DAC) sites open/closed post chemotherapy. C Differential accessibility of chromatin sites between treatment-naïve (pre) and post chemotherapy (post) samples. Coloured points indicate DACs (adjusted p < 0.01 and absolute log2FC > 0.25). Motif sequence logos presented for the top 3 motifs enriched within open/closed peak sites. D Aggregated accessibility profile of selected DACs stratified by treatment. Tracks Y scale represents normalised fragment count. E Within patient-cell-type average transcription factor motif chromVar activity score profile of motifs identified as differentially enriched (adjusted p < 0.01). F Intersections of differentially increased gene activity (expression) with enriched motifs in pre NACT treated tumour cells (top) and post NACT-treated tumour cells (bottom). G Aggregated accessibility profile of selected transcription factors.