Figure 4

All four murine tumor models exhibit reactivation of embryonic gene expression. The expression level of each gene in each sample was calculated relative to that in adult colon. Genes and samples were subjected to unsupervised hierarchical tree clustering for similarities among genes and tumors. (a) Heatmap shows the relative behaviors of 20,393 transcripts that passed basic signal quality filters with gene transcripts shown as separate rows and samples as separate columns. Note that the majority of genes over-expressed in tumors (red) are also over-expressed in embryonic colon; similarly, the genes under-expressed in tumors (blue) are under-expressed in embryonic colon. The color bars to the right indicate the position of 4,693 transcripts over-expressed in both tumors and development (red) or under-expressed in both (green). In addition, there are genes over-expressed in embryonic colon that are under-expressed in tumors and vice versa (asterisks). (b) The genes represented in (a) were divided into those over-expressed and under-expressed in embryonic colon and in the tumors, respectively. Fisher's exact test was used to calculate expected overlaps between lists and confirmed significant over-representation of development-regulated signatures among the tumors (*p < 1^-300, **p < 1.3^-19, ***p < 4^-296, ****p < 1^-300). (c) Heatmap showing the behavior of a subset of the transcripts in (a) (n = 4,693 features) that were over-expressed in both embryonic colon and tumor samples. Refer to Table 2 for a complete description of the genes associated with these clusters. (d) Embryonic gene expression can be further refined into genes expressed differentially during early (ED; E13.5-15.5) and late (LD; E16.5-18.5) embryonic development. Heatmap showing the relative behaviors of 750 transcripts that are highest-ranked for early versus late embryonic regulation. Overall, transcripts with the highest early embryonic expression were expressed at higher levels in nuclear β-catenin-positive tumors (A and M), whereas nuclear β-catenin-negative tumors (S and T) were representative of later stages of embryonic development. Sample groups: ED, early development (E13.5-E15.5); LD, late development (E16.5-E18.5); A, AOM-induced; M, Apc^Min/+; T, Tgfb1^-/-; Rag2^-/-; S, Smad3^-/-. Staging: nAC, normal colon. Clusters C8-C10 to the right of the heatmap correspond to the K-means functional clusters listed in Table 2.