Abstract
Predicting the distribution of metabolic fluxes in biochemical networks is of major interest in systems biology. Several databases provide metabolic reconstructions for different organisms. Software to analyze flux distributions exists, among others for the proprietary MATLAB environment. Given the large user community for the R computing environment, a simple implementation of flux analysis in R appears desirable and will facilitate easy interaction with computational tools to handle gene expression data. We extended the R software package BiGGR, an implementation of metabolic flux analysis in R. BiGGR makes use of public metabolic reconstruction databases, and contains the BiGG database and the reconstruction of human metabolism Recon2 as Systems Biology Markup Language (SBML) objects. Models can be assembled by querying the databases for pathways, genes or reactions of interest. Fluxes can then be estimated by maximization or minimization of an objective function using linear inverse modeling algorithms. Furthermore, BiGGR provides functionality to quantify the uncertainty in flux estimates by sampling the constrained multidimensional flux space. As a result, ensembles of possible flux configurations are constructed that agree with measured data within precision limits. BiGGR also features automatic visualization of selected parts of metabolic networks using hypergraphs, with hyperedge widths proportional to estimated flux values. BiGGR supports import and export of models encoded in SBML and is therefore interoperable with different modeling and analysis tools. As an application example, we calculated the flux distribution in healthy human brain using a model of central carbon metabolism. We introduce a new algorithm termed Least-squares with equalities and inequalities Flux Balance Analysis (Lsei-FBA) to predict flux changes from gene expression changes, for instance during disease. Our estimates of brain metabolic flux pattern with Lsei-FBA for Alzheimer’s disease agree with independent measurements of cerebral metabolism in patients. This second version of BiGGR is available from Bioconductor.
Highlights
We demonstrate the functionality of BiGGR by estimating metabolic fluxes in brain from measurements of metabolite exchange and gene expression in healthy humans and patients with Alzheimer’s disease. To this end we developed and demonstrate a new algorithm, termed Least-squares with equalities and inequalities Flux Balance Analysis (Lsei-FBA), which predicts changes in metabolic flux distribution from changes in gene expression between health and disease
To demonstrate the functionality of BiGGR, we conducted a flux balance analysis using a metabolic model that was previously used to study the effect of physical exercise on glucose and lactate metabolism in the human brain [10]
The model consists of 89 metabolites and 71 reactions representing the glycolytic pathway, the pentose phosphate pathway (PPP), the citric acid cycle, malate-aspartate shuttle, the glutamate and GABA shunt and oxidative phosphorylation in the brain and was assembled from the Recon 1 reconstruction database
Summary
If the biochemical reactions that operate in a cell type are known together with uptake or release measurements of some metabolites, the distribution of metabolic flux in the metabolic system can often be predicted. Large scale reconstructions of metabolic networks are valuable resources for building models for flux estimation. Genome-scale metabolic networks have been reconstructed for various organisms, such as microorganisms, animals and humans [1]. For instance the BioModels database [2] and the BiGG database [3], exist that store metabolic reconstructions in the standard modeling format SBML [4]. BiGG stores reconstructions of metabolism consisting of large lists of metabolites and reactions for H. sapiens, M. barkeri, S. cerevisiae, H. pylori, E. coli, P.putida, M. tuberculosis and S. aureus. The reconstructions recorded in these databases consist of genes, proteins, metabolites and reactions that are connected with each other, forming metabolic networks
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