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Using the Human Genome-Scale Metabolic Model Recon 2 for Steady-State Flux Analysis of Cancer Cell Metabolism

  • Lake-Ee QuekEmail author
  • Nigel TurnerEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1928)

Abstract

Flux analysis is performed to infer intracellular metabolic activity using measured rates. By applying the highly curated human metabolic reconstruction Recon 2 as the reference model, the investigation of cancer cell metabolic fluxes can encompass the full metabolic potential of a human cell. But in its full form, Recon 2 is unsuitable for conventional metabolic flux analysis due to a large number of redundant elements. Here, we describe a procedure to reduce Recon 2 to an appropriate scale for cancer cell flux analysis such that calculated flux intervals are still informative, without compromising the opportunity to explore alternative pathways encoded in Recon 2 that may reveal novel metabolic features.

Key words

Flux analysis Genome-scale model Constraint-based MATLAB COBRA Toolbox Cancer metabolism Model reduction 

Supplementary material

449903_1_En_25_MOESM1_ESM.xlsx (612 kb)
modelSpecs.xlsx . Spreadsheet containing Recon 2.2 and information required for model reduction (XLSX 611 kb)
449903_1_En_25_MOESM2_ESM.m (8 kb)
modelReduction.m . MATLAB script for model reduction (M 8 kb)
449903_1_En_25_MOESM3_ESM.m (3 kb)
monteCarloMFA.m . MATLAB script to perform Monte-Carlo flux analysis using the reduced model (M 3 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.School of Mathematics and StatisticsThe University of SydneySydneyAustralia
  2. 2.Department of Pharmacology, School of Medical SciencesUNSW AustraliaSydneyAustralia

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