Algorithms to infer metabolic flux ratios from fluxomics data

• Autor(a) principal: Carreira, Rafael
• Data de Publicação: 2013
• Outros Autores: Rocha, Miguel, Villas-Bôas, S. G., Rocha, I.
• Idioma: eng
• Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
• Texto Completo: http://hdl.handle.net/1822/33130
• topic: Biochemistry; Biology computing; Cellular biophysics; Genomics; 13C labeling distribution; Carbon atom transition maps; Constraint-based methods; Flux balance analysis; Fluxomics data; Genome-scale metabolic models; in silico cell simulation; Metabolic flux ratios; Metabolic network; Metabolite fragments; Reaction reversibility; Atomic measurements; Biochemistry; Bioinformatics; Carbon; Equations; Labeling; Vectors

In silico cell simulation approaches based in the use of genome-scale metabolic models (GSMMs) and constraint-based methods such as Flux Balance Analysis are gaining importance, but methods to integrate these approaches with omics data are still greatly needed. In this work, the focus relies on fluxomics data that provide valuable information on the intracellular fluxes, although in many cases in an indirect, incomplete and noisy way. The proposed framework enables the integration of fluxomics data, in the form of 13C labeling distribution for metabolite fragments, with GSMMs enriched with carbon atom transition maps. The algorithms implemented allow to infer labeling distributions for fragments/metabolites not measured and to build expressions for the relevant flux ratios that can be then used to enrich constraint-based methods for flux determination. This approach does not require any assumptions on the metabolic network and reaction reversibility, allowing to compute ratios originating from coupled joint points of the network. Also, when enough data do not exist, the system tries to infer ratio bounds from the measurements.