Relating perturbation magnitude to temporal gene expression in biological systems

Patterns of gene expression were measured in response to increasing sodium chloride concentrations (0, 0.5, 0.7, 1.0, and 1.2 M) for sixty genes impacted by osmotic shock. Expression of these genes was quantified over five time points using reverse transcriptase real-time polymerase chain reaction. Magnitudes of cumulative response for specific pathways, and the set of all genes, were obtained by combining the temporal response envelopes for genes exhibiting significant changes in expression with time. A linear relationship between perturbation magnitude and response was observed for the range of concentrations studied.This study develops a quantitative approach to describe the stability of gene response and pathways to environmental perturbation and illustrates the utility of this approach. The approach should be applicable to quantitatively evaluate the response of organisms via the magnitude of response and stability of the transcriptome to environmental change.The cause and effect relationship between perturbation and response is routinely used to study and characterize ecosystems in terms of stability. To extend this concept, we investigated the relationship between the affect of different perturbation magnitudes on the dynamic level of transcriptional response. The establishment of a quantitative relationship between stress and response has implications for predictive capabilities related to the behavior of organisms in natural and engineered systems and can be established on many levels including community, population, proteome, and transcriptome.Transcription is often compared by measuring the fold-change in relative expression [1,2]; however, a simple fold-change approach only accounts for one aspect of the response. Adjusting to perturbation spans a continuum of short-term stress responses, long-term acclimation, and genetic adaptation. Improved analytical tools for understanding the transcriptional mechanisms underlying variation in environmental toleranc