Fig. 2

Lower and upper first molar germs share temporal dynamics of gene expression. a Map of 16 transcriptomes from upper (black) and lower (gray) molar germs, at eight stages of development, on the two first principal components of a principal component analysis (PCA). PCA1 orders samples with time, hence represents shared temporal variation. PCA2 separates upper and lower molar germs. The percentage of variation explained by each axis is indicated. Lower and upper first molar pure-mesenchyme transcriptomes (pink) and epithelial cell transcriptomes (blue) projected on this map are segregating near upper and lower samples, respectively. b Ten main temporal profiles of expression determined independently for the lower (left) and upper (right) tooth. Ten clusters were obtained by K-mean clustering (see “Methods”) and associated number of genes are indicated. Cluster numbering and color are arbitrary and do not indicate a correspondence between lower and upper clusters. Each profile represents the median of relative expression level (normalized with expression level at ED 14.5) for all genes associated to a particular cluster. c Similarity of expression dynamics between upper and lower tooth. Left: The height of each bar corresponds to the number of genes which lower time profile is robustly assigned to one of the ten main “lower” clusters (Pearson R > 0.7). In black, the number of genes whose time profile in upper molar associates best (and with R > 0.7) to the same lower cluster: such genes have similar time profile during lower and upper molar development. In dark gray, the number of genes for which expression profile in upper data associates best (and with R > 0.7) to another lower cluster. In light gray, the number of genes, for which the upper expression profile is not well associated to any lower profile (R < 0.7). Right: the experiment was done in the opposite direction, starting with genes whose upper time profile is robustly associated to a given upper cluster and challenging their lower time profile