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• W2051676319 endingPage "e1002589" @default.
• W2051676319 startingPage "e1002589" @default.
• W2051676319 abstract "Understanding the complex regulatory networks underlying development and evolution of multi-cellular organisms is a major problem in biology. Computational models can be used as tools to extract the regulatory structure and dynamics of such networks from gene expression data. This approach is called reverse engineering. It has been successfully applied to many gene networks in various biological systems. However, to reconstitute the structure and non-linear dynamics of a developmental gene network in its spatial context remains a considerable challenge. Here, we address this challenge using a case study: the gap gene network involved in segment determination during early development of Drosophila melanogaster. A major problem for reverse-engineering pattern-forming networks is the significant amount of time and effort required to acquire and quantify spatial gene expression data. We have developed a simplified data processing pipeline that considerably increases the throughput of the method, but results in data of reduced accuracy compared to those previously used for gap gene network inference. We demonstrate that we can infer the correct network structure using our reduced data set, and investigate minimal data requirements for successful reverse engineering. Our results show that timing and position of expression domain boundaries are the crucial features for determining regulatory network structure from data, while it is less important to precisely measure expression levels. Based on this, we define minimal data requirements for gap gene network inference. Our results demonstrate the feasibility of reverse-engineering with much reduced experimental effort. This enables more widespread use of the method in different developmental contexts and organisms. Such systematic application of data-driven models to real-world networks has enormous potential. Only the quantitative investigation of a large number of developmental gene regulatory networks will allow us to discover whether there are rules or regularities governing development and evolution of complex multi-cellular organisms." @default.
• W2051676319 created "2016-06-24" @default.
• W2051676319 creator A5002873993 @default.
• W2051676319 creator A5008115010 @default.
• W2051676319 creator A5012212547 @default.
• W2051676319 creator A5042931108 @default.
• W2051676319 creator A5077715617 @default.
• W2051676319 date "2012-07-12" @default.
• W2051676319 modified "2023-10-11" @default.
• W2051676319 title "Efficient Reverse-Engineering of a Developmental Gene Regulatory Network" @default.
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