Fig. 3

Significantly different gene expression in EB, apical-LB, and basal-LB mesenchymal tissues. The heatmap displays gene clusters (y-axis) and sample clusters (x-axis). Genes and samples were both clustered by average linkage clustering using 1-Pearson’s correlation as a distance measure. Only genes that tested statistically significant for the overall model were used for cluster analysis. Fifteen gene clusters were chosen and colored using R’s rainbow function [72]. Each colored box represents gene expression in a single sample for a single probe set with yellow indicating high expression and red indicating low expression. Samples grouped according to cell population, with the first major division occurring between proximal basal samples (samples B2, B3, B5, and B6) and all other samples. The next major division separates proximal apical samples from the remaining samples, and the following division separates proximal samples from the basal samples. Within distal samples, EB and apical-LB samples clustered together