title: ÐÐ¾Ð´ÐµÐ»Ð¸ÑÐ¾Ð²Ð°Ð½Ð¸Ðµ Ð³ÐµÐ½Ð½Ð¾Ð¹ ÑÐµÑÐ¸
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð±Ð°ÐºÐ°Ð»Ð°Ð²ÑÐ°
titleType: Subtitle
title: Gene network modeling
Creators: name: Ð§ÐµÑÐ¿Ð°ÐºÐ¾Ð², ÐÐ¸ÑÐ°Ð¸Ð»
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2020
Subjects: Ð¼Ð°ÑÐµÐ¼Ð°ÑÐ¸ÑÐµÑÐºÐ¾Ðµ Ð¼Ð¾Ð´ÐµÐ»Ð¸ÑÐ¾Ð²Ð°Ð½Ð¸Ðµ
Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ñ
Ð´Ð½Ðº
ÑÐµÐ³ÑÐ»ÑÑÐ¸Ñ
ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ñ
mathematical modeling
optimization
dna
regulation
transcription

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description: This work is devoted to the use of mathematical modeling to study the effect of transcription factor binding sites on gene regulation. The review of modern methods for modeling gene expression is reviewed. The expression model proposed in the article by Kozlov et. al., 2015. The model was applied to describe the expression of the giant gene in Drosophila embryogenesis. The inverse modeling problem was numerically solved in different versions of this model, including different sets of binding sites for giant regulatory protein proteins. We examined sets consisting of binding sites ordered by protein affinity, and including a different proportion of the strongest sites: 100 % (the most complete set), 80 %, 50 %, 30 % and 10 %. The quality of each variant of the model was evaluated by the standard deviation of the solution from the data on the expression of the giant gene, obtained as a result of solving the inverse problem. Comparison of the calculation results showed that a model with 30% of sites is comparable with the original model in the quality of the description of experimental data. This means that for a correct description of the action of regulatory proteins on the giant gene, it is sufficient to take into account only a third of the regulatory region of this gene. The approach used in this work is an example of a quantitative analysis of the functionality of protein binding sites with DNA and can be generalized to other genes.