Venn Diagram of gene expression alterations for three comparisons. The tumor vs cell comparison showed the largest number of transcript expression changes, while the tumor compared to the adjacent normal tissues showed the lowest number. The 77 genes which show alterations in both the tumor vs cell and tumor vs normal are of interest. All comparisons were performed following RMA normalization of all raw image files. Following a 3-way ANOVA the sources of variation were removed and the comparisons conducted. Cut-off values for gene expression differences were p = 0.05 and combined with a > 2-fold change.