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. 2014 Nov 4;6(2):1286–1301. doi: 10.18632/oncotarget.2676

Figure 1. Concordant HER2-correlated changes in gene expression in cell lines and primary breast cancer tissue.

Figure 1

Expression array data from 812 primary breast cancers were collected, normalized and merged together (20). The 35% highest expressed HER2 samples are considered as HER2 positive and the 35% lowest expressed HER2 are considered as HER2 negative. The gene differential expression analysis was performed on HER2+ and HER2− tumor samples by LIMMA. 3350 significant genes with p-value less than 0.05 were selected and compared to 3350 transcripts with the most significant changes in cell lines (p < 0.05). Kappa analysis measured the significance of directionality for (A) MCF7HER2 vs primary tumors, (B) MDA453 vs primary tumors and (C) BT474 vs primary tumors.