Abstract
A novel approach to the dynamics of gene assemblies is presented. Central concepts are high-value genes; correlated activity; orderly unfolding of gene dynamics; dynamic mode decomposition; DMD unraveling dynamics. This is carried out for the Orlando et al. yeast database. It is shown that the yeast cell division cycle, CDC, only requires a six-dimensional space, formed by three complex temporal modal pairs: (1) a fast clock mother cohort; (2) a slower clock daughter cell cohort; and (3) an unrelated inherent gene expression. A derived set of sixty high-value genes serves as a model for the correlated unfolding of gene activity. Confirmation of this choice comes from an independent database and other considerations. The present analysis leads to a Fourier description, for the very sparsely sampled laboratory data. From this, resolved peak times of gene expression are obtained. This in turn leads to precise times of expression in the unfolding of the CDC genes. The activation of each gene appears as uncoupled dynamics originating in the mother and daughter cohorts, and of different durations. This leads to estimates of the composition of the original laboratory data. A theory-based yeast modeling framework is proposed, and additionally new experiments are suggested.