Fig. 8. GCPs, pre-neoplastic cells and tumor cells have distinct gene expression profiles. Gene expression in GCPs (four separate litters), pre-neoplastic cells (five mice), and tumor cells (five mice) from patched mutant mice, and adult cerebellum from wild-type mice (four mice), was analyzed using Affymetrix U74Av2 microarrays. Unsupervised principal components analysis (PCA) was used to assess the similarity in gene expression between these samples. (A) PCA plot of all 18 samples indicates that GCPs, pre-neoplastic cells and tumor cells are very similar to one another when compared with normal adult cerebellum. (B) Analysis excluding normal adult cerebellum suggests that compared with one another, GCPs, pre-neoplastic cells and tumor cells each have unique profiles of gene expression. (C) Single-linkage hierarchical clustering of the samples suggests that GCPs, pre-neoplastic cells and tumor cells are distinct, with pre-neoplastic and tumor cells resembling one another more closely than either resembles GCPs.