Computational reconstruction of metabolic networks from high-throughput profiling data

Diệp, Nguyễn Quỳnh; Hoan, Phạm Tho; Bao, Ho Tu; Hưng, Trần Đăng; Thắng, Phạm Quốc

doi:10.15625/1813-9663/27/1/460

Cited by 1 publication

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“…However, a metabolic reaction can involve more than two metabolites. Based on this reasoning, an attempt to also deduce triple interactions by using ternary mutual information was suggested (Diệp et al, 2011 ). Analysis of synthetic yeast glycolysis data and red blood cell data showed the success of this approach in capturing higher order interactions.…”

Section: Top-down Approaches To Discover Condition-specific Metabolicmentioning

confidence: 99%

Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

Çakır

Khatibipour

2014

Front. Bioeng. Biotechnol.

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The primary focus in the network-centric analysis of cellular metabolism by systems biology approaches is to identify the active metabolic network for the condition of interest. Two major approaches are available for the discovery of the condition-specific metabolic networks. One approach starts from genome-scale metabolic networks, which cover all possible reactions known to occur in the related organism in a condition-independent manner, and applies methods such as the optimization-based Flux-Balance Analysis to elucidate the active network. The other approach starts from the condition-specific metabolome data, and processes the data with statistical or optimization-based methods to extract information content of the data such that the active network is inferred. These approaches, termed bottom-up and top-down, respectively, are currently employed independently. However, considering that both approaches have the same goal, they can both benefit from each other paving the way for the novel integrative analysis methods of metabolome data- and flux-analysis approaches in the post-genomic era. This study reviews the strengths of constraint-based analysis and network inference methods reported in the metabolic systems biology field; then elaborates on the potential paths to reconcile the two approaches to shed better light on how the metabolism functions.

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Section: Top-down Approaches To Discover Condition-specific Metabolicmentioning

confidence: 99%

Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

Çakır

Khatibipour

2014

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

show abstract

Computational reconstruction of metabolic networks from high-throughput profiling data

Cited by 1 publication

References 21 publications

Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

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