Dataset Information

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation.

ABSTRACT: The extensive heterogeneity of biological data poses challenges to analysis and interpretation. Construction of a large-scale mechanistic model of Escherichia coli enabled us to integrate and cross-evaluate a massive, heterogeneous dataset based on measurements reported by various groups over decades. We identified inconsistencies with functional consequences across the data, including that the total output of the ribosomes and RNA polymerases described by data are not sufficient for a cell to reproduce measured doubling times, that measured metabolic parameters are neither fully compatible with each other nor with overall growth, and that essential proteins are absent during the cell cycle-and the cell is robust to this absence. Finally, considering these data as a whole leads to successful predictions of new experimental outcomes, in this case protein half-lives.

SUBMITTER: Macklin DN

PROVIDER: S-EPMC7990026 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Simultaneous cross-evaluation of heterogeneous <i>E. coli</i> datasets via mechanistic simulation.

Macklin Derek N DN Ahn-Horst Travis A TA Choi Heejo H Ruggero Nicholas A NA Carrera Javier J Mason John C JC Sun Gwanggyu G Agmon Eran E DeFelice Mialy M MM Maayan Inbal I Lane Keara K Spangler Ryan K RK Gillies Taryn E TE Paull Morgan L ML Akhter Sajia S Bray Samuel R SR Weaver Daniel S DS Keseler Ingrid M IM Karp Peter D PD Morrison Jerry H JH Covert Markus W MW

Science (New York, N.Y.) 20200701 6502

The extensive heterogeneity of biological data poses challenges to analysis and interpretation. Construction of a large-scale mechanistic model of <i>Escherichia coli</i> enabled us to integrate and cross-evaluate a massive, heterogeneous dataset based on measurements reported by various groups over decades. We identified inconsistencies with functional consequences across the data, including that the total output of the ribosomes and RNA polymerases described by data are not sufficient for a ce ...[more]

PMID: 32703847

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Dataset Information

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation.

Publications

Simultaneous cross-evaluation of heterogeneous <i>E. coli</i> datasets via mechanistic simulation.

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