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Therefore, to identify genes that exhibit differential expression between stages, we tracked the expression trajectory for each expressed gene in pair-wise comparisons between successive stages.
Thus, to identify genes that are differentially expressed at stage transitions, we followed the expression trajectory of every gene by performing pairwise comparisons of their expression between successive stages.
We observed that the majority of infected macrophages and phagocytosed C. albicans pairs followed a linear expression trajectory between two major endpoints or clusters, recapitulating the two major infection co-stages; some cells exhibited alternative expression paths, suggesting the existence of minor cell trajectories (Fig. 4b; Supplementary Figure 11).
A linear model, fit to each probe-set expression value, was used to impute the gene expression trajectory over the entire follow-up period.
In this paper, we apply novel statistical methods [17] to identify genes for which the expression trajectory predicts respiratory recovery, and then we relate these genes to the networks and pathways to which they belong.
The scrambled sequences were constructed such that they never depicted any coherent expression trajectory and image transitions could not be predicted from the preceding transitions.
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Nowakowski, T. J. et al. Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex.
PI controllers would need to operate under very high gain settings to achieve an equally fast rise, however, this would inevitably result in large oscillations around the target levels (Supplementary Note 4). Figure 2: Tracking of reference sfGFP expression trajectories.
We address this challenge by building a chemical kinetic model that utilizes information encoded in the stochastic protein expression trajectories typically measured in experiments.
In addition, it has remained unclear whether the anatomically distinct anterior and posterior lobes of the submaxillary gland are evolving on separate gene expression trajectories or if they remain under the shared genetic control.
Fig. 3 presents three "branchings" of gene expression trajectories during the pancreas cell differentiation.
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