Fig. 4: TFs contributes to the activation of Metastatic-specific enhancer.

a Scheme of the ATAC-seq and RNA-seq data integration workflow using the IMAGE machine learning approach (created with BioRender.com). b Clustering of top MD-associated motifs with a motif activity MD > tIMEC and XD cells and defined as causal for gene regulation with an FDR < 0.01. Additional columns show z-score normalized expression of motif-associated TF, PCC between motif activity, and gene expression of associated TF and the associated TF family. Dot size for the TF family indicates enrichment in the unfiltered list by hypergeometric t-test. c Violin plots showing activity of MD-enriched motifs in tIMEC, XD, and MD cells, with an activity MD > tIMEC/XD. d Violin plots showing normalized expression values of motif-associated TFs showing a higher motif activity in MD compared to tIMEC or XD. e, f Distribution plot showing the rank of the TFs identified as drivers of MD enhancer activity among all TFs considered for the analysis (e) or expressed in the TCGA BC dataset (f). g Density plots showing the SOX9 CUT&RUN signal in the four differential ATAC-seq clusters identified. Signal distribution is centered on the TSS peak and ranges from −5kB to 5kB. Greyscale signal intensity legend is valid for the three cell lines. h Cumulative plots showing SOX9 CUT&RUN signal at peaks identified by ATAC-seq for the four defined clusters. i Representation of SOX9 iCD in MD cells. Vertices colors represent SOX9-linked enhancers (light blue), enhancers (gray), and promoters (yellow). The grayscale of edges is proportional to the number of connections between vertices. The violin plots in (c) and (d) indicate median values (middle lines), first and third quartiles (dashed lines). Statistical significance was determined by one-tailed unpaired student’s t-test.