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Conversely, the population transferred to Medium T was pulled toward Attractor 2. This shift is also adaptive since the high mDHFR expression compensates for tetrahydrofolate depletion in Medium T. Note that the control transfer to Medium N supplemented with the same concentration of nalidixic acid resulted in a stochastic shift of gene expression toward that of either Attractor 1 or 2 (Figure 2).
This may, in turn, lead to the observed shift of gene expression among tissues.
Nevertheless, our important observation remains the striking correlation between the anterior shift of gene expression patterns, and the fusion of basal bones into a single metapterygium.
Interestingly, Roy showed a shift of gene expression towards collagen IV and fibronectin expression in vitro (endothelial cells) and in diabetic rats (kidney cortex and myocardium) [ 15] with a similar design of a period with poor control followed by normalized glucose levels.
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And although there might be an enticing link between transcript down-regulation upon the diauxic shift of genes such as HXK2 and PFK2[ 55] and their role in glycolytic oscillations, this relationship is not as straightforward.
The problem with this common-sense standardization is that it misses out on global shifts of gene expression, such as those initiated by potent regulators such as c-Myc.
Compared to previously reported mathematical approaches, the combination of these methods also facilitated the detection of modified amplitudes and phase-shifts of gene expression.
A higher enrichment score corresponds to a shifting of gene set constituents towards either end of the ranked list representing strongly positive or negative correlations.
These extensions allow the shifting of gene expression patterns up to K symbols up and down, in order to potentially find maximal e-CCC-Biclusters that would not be found due to different gene expression rates.
Among all 237 patients, there was variability in expression shifts of genes expressed in the basal layer (ITGA6, KRT5, KRT14), granular layer and cornified envelope (IVL, LOR, FLG), and early KC differentiation genes (KRT1, KRT10, DSG1, DSC1) (Additional file 7).
The important result is that we have two cases of an anterior shift: (a) the comparison between sharks and tetrapods, (b) the RA-treated shark buds, and in both cases two important observations are correlated: (i) the anterior shifting of genes, (ii) a reduction or loss of anterior basal bones, leaving a metapterygium-dominated arrangement.
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