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Fig. 1 | Breast Cancer Research

Fig. 1

From: Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas

Fig. 1

Differential chromatin accessibility between ER+ /HER2- ILC and ER+/HER2- IDC. A PCA of ATAC-seq signal in all peaks (n = 204,728). All tumors of ER+ were clustered together, but ILC and IDC tumors were slightly separated. The three outliers of ER+/HER2- IDCs and one outlier of ER+/HER2+ IDCs are annotated in the plot. B Volcano plot of ATAC-seq peaks comparing ILCs (n = 13) to IDCs (n = 27). Significant peaks with differential chromatin accessibility are highlighted in red. The vertical dotted line indicates an absolute log2 fold change of 1.0 and the horizontal dotted line indicates an FDR-corrected p value 0.05 criterion; the DA peaks enriched in ILCs (n = 5,124) vs IDCs (n = 6,638). FDR-corrected p values were obtained using DESeq2. C Hierarchical clustering of the 11,762 DA peaks. The significant DA peaks identified in Fig. 1B were aggregated to 11,762 peaks and represented as chromatin accessibility patterns in ILCs and IDCs. Colors represent log2-transformed peak count data and the z-score row was normalized. D Pie charts show the percentage of DA ATAC-seq peaks (FDR < 0.05) at the promoter, intronic, intergenic, and exonic regions for ILCs versus IDCs. E Enrichment of TF-binding motifs for the subclusters of DA regions of ILCs and IDCs. The top 10 enriched motifs are shown. F Enrichment of PANTHER pathways for subclusters of DA regions of ILCs and IDCs. In the bar plot, the gray line indicates the significance of the PANTHER pathways (hypergeometric test, adjusted p value < 0.05). GREAT was used to identify the PANTHER pathways overrepresented in the DA peaks

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