Figure 4.

Two-dimensional hierarchical clustering of cultured cell and tissue samples using Pearson's (centered) correlation and average linkage, based on 1252 probe sets that were significantly different (q ≤ 0.05) between TDE_CC and TDF_SM cell strains used to cluster all of the individual samples indicated by the blue, yellow, red, and green bars. Analyzed cell samples were from 2D monolayer cultures of comparably passaged TDE_CC and TDF_SM cells, respectively, harvested when at 60% and 70% confluence on collagen type I–coated plastic. BDEsp-T refers to parent tumor tissue from which the TDE_CC cholangiocarcinoma and TDF_SM myofibroblastic cell strains were derived, whereas NL refers to corresponding pair-matched right liver lobe tissue samples without histological evidence of cholangiocarcinoma. Each of the colored rows in the heat map shows the relative expression for that specific gene in the separate specimen samples (columns), where the relative extent of gene overexpression is indicated in red and that of gene underexpression is shown in green when compared to the median intensity across all samples. The gray sidebars reflect common probe sets overexpressed in both the TDE_CC cell strain and BDEsp-T tissue samples relative to TDF_SM and NL; the black side bar emphasizes genes commonly overexpressed in the TDF_SM cells and BDEsp-T tumor compared with TDE_CC and NL.