Independent microarray analyses identify new targets of Runx2 and CBFβ in metastatic MDA-MB-231 cells. (A) Fluorescence microscopy showing co-localization of Runx2 and CBFβ in the nucleus of MDA-MB-231 cells. MDA-MB-231 cells were immunostained with specific antibodies as indicated. Nuclei (blue) were stained with DAPI. (B) Western blot showing siRNA knockdown of Runx2 and CBFβ. The upper panel shows total cell lysates derived from siRNA transfections of MDA-MB-231 cells after immunodetection with anti-Runx2 or anti-CBFβ antibodies. The lower panel is a Tubulin loading control. (C) Volcano plots of differentially expressed genes in MDA-MB-231 cells treated with siRNAs against Runx2 (siRunx2) or CBFβ (siCBFβ) vs non-specific siRNA control (siNS). The q values were plotted against fold suppression/induction. The darker vertical line indicates a cut off of ≥ 2-fold change and the darker horizontal line represents a q value ≤ 0.05. Each point represents an individual transcript. (D) Hierarchical clustering analysis. The colour bar indicates the relative abundance of each transcript with red being the most abundant.