Fig. 2

Accessibility at FOX and SOX Binding Sites Define Tumor Groups. A) Table displaying top motif result from HOMER for each chromatin signature. Due to similarity across SOX and FOX binding motifs, we refer to SOX6 simply as SOX, and FOXM1 simply as FOX. P-values obtained within HOMER. B) Profile plots depicting average accessibility of tumor groups in motif regions across all accessible peak regions in tumors, indicating that group 1 and 2 tumors show increased accessibility at SOX and FOX motifs, respectively. We again use the SOX6 motif to represent SOX motifs, and the FOXM1 motif to represent FOX motifs. Regions with no signal were ignored in the calculation of average accessibility. C) Heatmap showing expression of SOX and FOX factors across tumor groups. Factors are ordered from 1 to 10 by standard deviation across tumors. D) Heatmaps showing binding of FOXA1, ER, and H3K27ac in MCF-7 cells within regions from signatures 1, 2 and 3. Data from ChIP-Seq of MCF-7 cells; regions sorted from greatest to least FOXA1 enrichment.