title: Analysing Algorithms and Data Sources for the Tissue-Specific Reconstruction of Liver Healthy and Cancer Cells.
abstract: Genome-Scale Metabolic Models (GSMMs), mathematical representations of the cell metabolism in different organisms including humans, are resourceful tools to simulate metabolic phenotypes and understand associated diseases, such as obesity, diabetes and cancer. In the last years, different algorithms have been developed to generate tissue-specific metabolic models that simulate different phenotypes for distinct cell types. Hepatocyte cells are one of the main sites of metabolic conversions, mainly due to their diverse physiological functions. Most of the liver's tissue is formed by hepatocytes, being one of the largest and most important organs regarding its biological functions. Hepatocellular carcinoma is, also, one of the most important human cancers with high mortality rates. In this study, we will analyze four different algorithms (MBA, mCADRE, tINIT and FASTCORE) for tissue-specific model reconstruction, based on a template model and two types of data sources: transcriptomics and proteomics. These methods will be applied to the reconstruction of metabolic models for hepatocyte cells and HepG2 cancer cell line. The models will be analyzed and compared under different perspectives, emphasizing their functional analysis considering a set of metabolic liver tasks. The results show that there is no "ideal" algorithm. However, with the current analysis, we were able to retrieve knowledge about the metabolism of the liver.
authors.affiliation: Centre Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
authors.forename: Jorge
authors.initials: J
authors.lastname: Ferreira
authors.affiliation: Centre Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
authors.forename: Sara
authors.initials: S
authors.lastname: Correia
authors.affiliation: Centre Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal. mrocha@di.uminho.pt.
authors.forename: Miguel
authors.initials: M
authors.lastname: Rocha
mesh_terms: D000465:Algorithms; D006528:Carcinoma, Hepatocellular / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D006801:Humans; D008113:Liver Neoplasms / Q000378:metabolism*; D008954:Models, Biological; D008962:Models, Theoretical
keywords: Hepatocellular carcinoma; Liver metabolism; Tissue-specific genome-scale metabolic models