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Background  This paper lies in the context of modeling the evolution of gene expression away from stationary states, for example in systems subject to external perturbations or during the development of an organism. We base our analysis on experimental data and proceed in a top-down approach, where we start from data on a system's transcriptome, and deduce rules and models from it without  a priori  knowledge. We focus here on a publicly available DNA microarray time series, representing the transcriptome of  Drosophila  across evolution from the embryonic to the adult stage.    Results  In the first step, genes were clustered on the basis of similarity of their expression profiles, measured by a translation-invariant and scale-invariant distance that proved appropriate for detecting transitions between development stages. Average profiles representing each cluster were computed and their time evolution was analyzed using coupled differential equations. A linear and several non-linear model structures involving a transcription and a degradation term were tested. The parameters were identified in three steps: determination of the strongest connections between genes, optimization of the parameters defining these connections, and elimination of the unnecessary parameters using various reduction schemes. Different solutions were compared on the basis of their abilities to reproduce the data, to keep realistic gene expression levels when extrapolated in time, to show the biologically expected robustness with respect to parameter variations, and to contain as few parameters as possible.    Conclusions  We showed that the linear model did very well in reproducing the data with few parameters, but was not sufficiently robust and yielded unrealistic values upon extrapolation in time. In contrast, the non-linear models all reached the latter two objectives, but some were unable to reproduce the data. A family of non-linear models, constructed from the exponential of linear combinations of expression levels, reached all the objectives. It defined networks with a mean number of connections equal to two, when restricted to the embryonic time series, and equal to five for the full time series. These networks were compared with experimental data about gene-transcription factor and protein-protein interactions. The non-uniqueness of the solutions was discussed in the context of plasticity and cluster versus single-gene networks.

Robust non-linear differential equation models of gene expression evolution across Drosophila development