Fig. 2

Heatmaps based on mean, normalised expression of selected factors representing ‘signals’ and ‘switches’. a All homeobox transcription factors [35]. b Wnt, Notch and Hedgehog signalling components [35, 63, 178]. c Differentially expressed genes of interest (Table 2, Additional file 4: Table S4; note that some of the factors in a, b were differentially expressed in one or more of the contrasts and are therefore also represented in c). All three suites of genes produce the same hierarchical clustering of the samples, congruent with that based on overall gene expression (Fig. 1c)