Figure 5

Microarray gene expression data mining: hierarchical clustering and functional network analysis. (A) Hierarchical clustering analysis of gene expression profiles in MCF-7, MCF-7-14 and MDA-MB-231 cell lines. Columns represent the 13,092 probe sets detected in all samples. Measurements of each probe were normalized to the median of the probe measurements in MCF-7, MCF-7-14 and MDA-MB-231 cell lines. The intensity of bar colors indicates the degree of gene upregulation (red) or downregulation (green). Although the MCF-7-14 cell gene expression profile was more similar to that of MCF-7 cells than to MDA-MB-231 cells, there were some similarities between MCF-7-14 and MDA-MB-231 cells in gene expression (black flames). (B) To identify potentially important differences in biological mechanisms regarding their invasive potential, we selected 163 probe sets up- (red, see Additional file 2) or downregulated (green, see Additional file 3) >2-fold in both MCF-7-14 and MDA-MB-231 cells compared with MCF-7 cells. Results are represented relative to mRNA levels of MCF-7 cells. (C) The most significant network of 163 probe sets (144 unique genes) constructed using IPA 5.0 (see Additional file 4). Gene network is represented as nodes and lines between two nodes. Node shapes symbolize the functional class of the gene product: square, cytokine; diamond, enzyme; inverted triangle, kinase; rectangle, nuclear receptor; ellipse, transcription regulator; circle, other. The intensity of node colors indicates the degree of upregulation (red) or downregulation (green). Continuous and dashed lines indicate direct and indirect interactions between molecules, respectively. Bold nodes represent multiple-mapped genes (see also Table 1) or selected interesting genes.