Abstract
Understanding the molecular mechanisms involved in gene regulation is one of the basic issues of systems biology. Conventional approaches to modeling gene regulation often fail to distinguish between the model properties that adequately reflect the characteristics of a biological system and those associated with the nature of the model. A logical approach was developed for modeling the regulation of gene expression, which provides maximal further use of the available empirical data and minimal use of a priory hypotheses. Rules of gene regulation were formulated in the form of linguistic conditions, that is, in a language similar to human languages. Fuzzy linguistic modeling (FLM) was used as a method that more accurately reflects the actual data. This study is the first to employ FLM in constructing models of the activities of cis-regulatory modules (CRMs) and to apply the method to the problems related to expression of genes involved in biochemical patterning of embryos. Essential details were thus clarified for the mechanisms by which primary morphological gradients are read by a combination of two or more cis-regulatory modules of the same gene.
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