Fig. 3

The upper molar germ is enriched in mesenchyme. a Boxplot showing the distribution of an index of mesenchyme specificity, for the totality of genes (white) and for genes more expressed in upper (black) or in lower (gray) molar germ. This index was measured as the ratio of expression levels between mesenchyme and epithelium (median of log ratio(mesenchyme/epithelium) at 12.0, 13.0, and 13.5 dpc, estimated using microarray data [39]. non-DE genes non-significantly biased between upper and lower tooth, All genes significantly biased for at least one stage, DE 1 or 2 stages genes significantly biased for one or two developmental stages, DE all stages genes significantly biased for all developmental stages. b Mesenchyme proportions estimated from deconvolutions for our eight developmental stages. Markers were obtained from bite-it database (11 for EK, 12 for epithelium, and 14 for mesenchyme). Confidence intervals were extracted by resampling (500 bootstraps). RNA-seq samples of mesenchyme isolated from lower and upper molar germs [45] were used as positive controls. c Boxplot showing the difference between mesenchyme proportion between 24 pairs of upper and lower molar germs, taken between ED 14.5 and ED 17.5. Mesenchyme proportion is expressed as a percentage of mesenchyme volume relative to total germ volume, as measured on complete series of histological sections. d Map showing the location of the genes on the two first principal components of a PCA analysis obtained from upper (black) and lower (gray) molar germs, at eight stages of development. The interpretation of PCA axes (developmental timing for PCA1 and upper/lower for PCA2, respectively) is reminded with arrows. Genes are colored according to their tissue-specificity in a tissue specific dataset ([39]; expressed mesenchyme > epithelium in pink; expressed epithelium > mesenchyme in blue)