A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.

ABSTRACT: To understand the relationship between an enhancer DNA sequence and quantitative gene expression, thermodynamics-driven mathematical models of transcription are often employed. These "sequence-to-expression" models can describe an incomplete or even incorrect set of regulatory relationships if the parameter space is not searched systematically. Here, we focus on an enhancer of the Drosophila gene ind and demonstrate how a systematic search of parameter space can reveal a more comprehensive picture of a gene's regulatory mechanisms, resolve outstanding ambiguities, and suggest testable hypotheses. We describe an approach that generates an ensemble of ind models; all of these models are technically acceptable solutions to the sequence-to-expression problem in light of wild-type data, and som

SUBMITTER: Samee MA 

PROVIDER: S-EPMC5094195 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature