Fig. 4

Time-dependent differences in upper/lower gene expression. a Number of differentially expressed genes for seven consecutive periods. We defined these seven periods by considering pairs of consecutive developmental stages as replicates (i.e. ED14.5–15.0, ED15.0–15.5, etc.). We extracted differentially expressed genes at each of these seven periods and split genes into two categories: those with a higher expression level in lower molar and those with a higher expression level in upper molar. We also split genes that were found to be differentially expressed at 1, 2, …, up to all (7) periods. b Distribution of temporal shifts of the upper/lower expression ratios, extracted by a method based on hidden Markov model. The size of the spots is proportional to the number of genes for which the upper/lower expression ratio follows a particular kind of profile. For instance, small–large at 14.5–15 indicates that the upper/lower expression ratio was small at ED 14.5 and larger at stage ED 15. c Classes and number of genes assigned to 8 temporal profiles for the genes that are differentially expressed at ED 15.5–16.0 but not earlier or later during the developmental series