Gene expression profiling of Int6sh-expressing hyperplasias and tumors. (a) Total RNA from wild-type, hyperplasia-containing and tumor-containing transgenic mammary glands was prepared and pools were made consisting of five mice each. The following comparisons were performed on Agilent Mouse 22 K 60-mer Oligo Arrays (G4121A): wild-type pregnant mammary glands vs Int6sh transgenic mammary glands at 18 months of age containing persistent hyperplasia; non-pregnant wild-type age/parity-matched mammary glands vs Int6sh persistent hyperplastic glands; Int6sh hyperplastic glands vs undifferentiated tumors and Int6sh hyperplastic glands vs adenocarcinomas. The colored spheres show the number of genes that are at least twofold up or downregulated in each one of these comparisons. The numbers in the intersected spaces denotes genes that are common to any particular pairwise comparison. (b) The expression heatmap and gene list at the bottom of the figure shows those genes found to be coordinately regulated throughout Int6sh-induced mammary tumorigenesis. The GeneSpring expression clustering algorithm was employed to determine which genes show the same pattern of expression in the four conditions, denoted A, B, C and D, corresponding to the comparisons shown in (a). The color bar on the left shows how hue relates to direction and extent of the transcriptional differences. Functional groups font color key: dark orange, protein folding and degradation; light blue, solute transporters; purple, neuronal guidance; red, energy metabolism; lime green, adipose, lipid and fatty acid metabolism; dark blue, cell cycle regulation; green, chromatin architecture and chromosome segregation. Asterisks denote genes that have been previously implicated in mammary tumorigenesis.