Statistical inference in ensemble modeling of cellular metabolism

PLoS Comput Biol. 2019 Dec 9;15(12):e1007536. doi: 10.1371/journal.pcbi.1007536. eCollection 2019 Dec.

Abstract

Kinetic models of metabolism can be constructed to predict cellular regulation and devise metabolic engineering strategies, and various promising computational workflows have been developed in recent years for this. Due to the uncertainty in the kinetic parameter values required to build kinetic models, these workflows rely on ensemble modeling (EM) principles for sampling and building populations of models describing observed physiologies. Sensitivity coefficients from metabolic control analysis (MCA) of kinetic models can provide important insight about cellular control around a given physiological steady state. However, despite considering populations of kinetic models and their model outputs, current approaches do not provide adequate tools for statistical inference. To derive conclusions from model outputs, such as MCA sensitivity coefficients, it is necessary to rank/compare populations of variables with each other. Currently existing workflows consider confidence intervals (CIs) that are derived independently for each comparable variable. Hence, it is important to derive simultaneous CIs for the variables that we wish to rank/compare. Herein, we used an existing large-scale kinetic model of Escherichia Coli metabolism to present how univariate CIs can lead to incorrect conclusions, and we present a new workflow that applies three different multivariate statistical approaches. We use the Bonferroni and the exact normal methods to build symmetric CIs using the normality assumptions. We then suggest how bootstrapping can compute asymmetric CIs whilst relaxing this normality assumption. We conclude that the Bonferroni and the exact normal methods can provide simple and efficient ways for constructing reliable CIs, with the exact normal method favored over the Bonferroni when the compared variables present dependencies. Bootstrapping, despite its significantly higher computational cost, is recommended when comparing non-normal distributions of variables. Additionally, we show how the Bonferroni method can readily be used to estimate required sample numbers to attain a certain CI size.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cells / metabolism
  • Computational Biology
  • Computer Simulation
  • Confidence Intervals
  • Escherichia coli / metabolism*
  • Kinetics
  • Metabolism
  • Models, Biological*
  • Systems Biology
  • Uncertainty

Grant support

TH and VH were supported by the Ecole Polytechnique Fédérale de Lausanne (EPFL) and the Swiss National Science Foundation grant 315230_163423. MOB was supported by the University of Lausanne. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.