Nevertheless, a number of genes had prominence-specific expression patterns, particularly Fap with a unique expression profile in each prominence (Figure 14C).
Transcripts encoding p63 were lowest in the FNP reflecting the slower rate of change between keratins characteristic of simple versus stratified epithelia in this prominence (Figure 10C).
With respect to the MdP, our analysis showed that several genes required for muscle differentiation [29] including Tcf21 (capsulin, GeneID: 21412), Myf5 (GeneID: 17877), Myod1 (GeneID: 17927), Myog (GeneID: 17928) and Msc (GeneID: 17681), were expressed at higher levels in this prominence (Figure 18A).
The expression of a much larger group of genes was up-regulated in all prominences (Figure 17C).
A more limited number of probes were expressed in only one prominence or were shared between two of the three prominences (Figure 2).
In the MxP, Col9a2 (GeneID: 12840) transcript levels remained relatively flat throughout the time course, whilst this gene showed increasing levels in the other prominences (Figure 11D).
Only two collagens, Col2a1 (GeneID: 12824) and Col18a1 (GeneID: 12822), showed a downward trend of expression in all prominences (Figure 11A).
Though expression of a small number of collagen genes decreased over time, or remained level (Figure 11A, B), a majority of these genes displayed co-ordinate up-regulation of transcript levels in the three prominences (Figure 11C and Figure S4).
The microarray data were also processed to ascertain those transcription factor genes that exhibited prominence-specific expression or were coordinately regulated in any two of the three prominences (Figure 18, and Figures S7 and S8).
In contrast, the expression profiles for many other genes encoding adherens and tight junction proteins [35], [36] displayed markedly different dynamics in the FNP from the other two prominences (Figure 15D).
