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. Author manuscript; available in PMC: 2021 Jun 18.
Published in final edited form as: Mol Cell. 2020 May 23;78(6):1114–1132.e10. doi: 10.1016/j.molcel.2020.04.034

Figure 3. Transcriptome Profiling Identifies Matrisome Network Genes Generally Upregulated by BRD4-S but Downregulated by BRD4-L.

Figure 3.

(A) RNA-seq flowchart and DEG classification. RNA-seq data were from MDA-MB-231 with or without BRD4 isoform-specific knockdown.

(B) Top canonical pathways identified for BRD4-S/L DEGs highlighting S-unique-upregulated matrisome network (red) and L-preferred-downregulated core ECM (blue).

(C) Heatmap of top DEGs from MDA-MB-231 RNA-seq divided into up and downregulated (Dn) groups, each in triplicate. Scale bar is based on the Z score of CPM (counts per million).

(D) List of BRD4-S-upregulated matrisome genes with significantly higher expression in IDC vs. normal breast samples (P values from Oncomine METABRIC 2136 BCa dataset).

(E) Unique gene families identified in BRD4-S-upregulated RNA-seq from MDA-MB-231.

(F) Kaplan-Meier plot showing higher expression of a 17-matrisome-gene signature identified in S-Up predicts unfavorable DMFS in basal subtype patients. The 17 DEGs analyzed are indicated.