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• W2790753957 endingPage "e1006962" @default.
• W2790753957 startingPage "e1006962" @default.
• W2790753957 abstract "Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory events. Since the pioneering work of Covert and co-workers as well as Shlomi and co-workers it is debated, how regulation and metabolism synergistically characterize a coherent cellular state. The first approaches started from metabolic models which were extended by the regulation of the encoding genes of the catalyzing enzymes. By now, bioinformatics databases in principle allow addressing the challenge of integrating regulation and metabolism on a system-wide level. Collecting information from several databases we provide a network representation of the integrated gene regulatory and metabolic system for Escherichia coli, including major cellular processes, from metabolic processes via protein modification to a variety of regulatory events. Besides transcriptional regulation, we also take into account regulation of translation, enzyme activities and reactions. Our network model provides novel topological characterizations of system components based on their positions in the network. We show that network characteristics suggest a representation of the integrated system as three network domains (regulatory, metabolic and interface networks) instead of two. This new three-domain representation reveals the structural centrality of components with known high functional relevance. This integrated network can serve as a platform for understanding coherent cellular states as active subnetworks and to elucidate crossover effects between metabolism and gene regulation." @default.
• W2790753957 created "2018-03-29" @default.
• W2790753957 creator A5003070798 @default.
• W2790753957 creator A5021938434 @default.
• W2790753957 creator A5069994430 @default.
• W2790753957 creator A5084385844 @default.
• W2790753957 date "2019-05-03" @default.
• W2790753957 modified "2023-10-02" @default.
• W2790753957 title "A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli" @default.
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• W2790753957 doi "https://doi.org/10.1371/journal.pcbi.1006962" @default.
• W2790753957 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6519848" @default.
• W2790753957 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/31050661" @default.
• W2790753957 hasPublicationYear "2019" @default.
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• W2790753957 hasAuthorship W2790753957A5003070798 @default.
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