Generalized framework for context-specific metabolic model extraction methods

• Main Authors: Semidán eRobaina Estévez, Zoran eNikoloski
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2014-09-01
• Series: Frontiers in Plant Science
• Subjects: data integration; high-throughput data; Genome-scale models; mathematical programming; context-specific models
• Online Access: http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00491/full

Genome-scale metabolic models are increasingly applied to investigate the physiology not only of simple prokaryotes, but also eukaryotes, such as plants, characterized with compartmentalized cells of multiple types. While genome-scale models aim at including the entirety of known metabolic reactions, mounting evidence has indicated that only a subset of these reactions is active in a given context, including: developmental stage, cell type, or environment. As a result, several methods have been proposed to reconstruct context-specific models from existing genome-scale models by integrating various types of high-throughput data. Here we present a mathematical framework that puts all existing methods under one umbrella and provides the means to better understand their functioning, highlight similarities and differences, and to help users in selecting a most suitable method for an application.