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The prospect of imaging the single chromosome at the nanoscale level will aid not only the direct visualization but also spatial characterization of the configuration of genes within the chromatin.
Thus, it is not possible to compare the configuration of genes involved in PD and aging at present.
In some cases the orientation of genes in modules residing outside the cluster in one species matches the configuration of genes in a different species.
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Genome rearrangements influence gene order and configuration of gene clusters in all genomes.
Here g i (t) is the configuration of gene i at time t.
Assuming steady state dynamics would collapse the trajectories representing these shifts into a single attractor point at the final configuration of gene expression.
As an alternative, we asked whether the spatial configuration of gene copies within the nucleus could affect siRNA formation; such an effect would provide strong evidence for the formation of dsRNA in the nucleus.
Our model performs significantly better with data from the true distribution, suggesting that our predictions are due to the specific configuration of gene expression and the metabolites that we are testing and not due to a global trend in the expression data.
However, there is little work on characterizing configurations of genes that are eligible to be a cluster according to a given definition.
Empirical data strongly support the notion that, there are adaptive reasons to keep certain configurations of genes together over evolutionary time [ 37].
To identify the attractors of each model, we used the program Atalia [[ 56]; freely available] by following the dynamics of all possible initial configurations of gene expression.
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