ArticleBioinformatics (Oxford, England)2011
The strength of chemical linkage as a criterion for pruning metabolic graphs.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- Finding branched pathways in metabolic network via atom group tracking.PLoS computational biology · 2021Article
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Abstract
motivationA metabolic graph represents the connectivity patterns of a metabolic system, and provides a powerful framework within which the organization of metabolic reactions can be analyzed and elucidated. A common practice is to prune (i.e. remove nodes and edges) the metabolic graph prior to any analysis in order to eliminate confounding signals from the representation. Currently, this pruning process is carried out in an ad hoc fashion, resulting in discrepancies and ambiguities across studies.
resultsWe propose a biochemically informative criterion, the strength of chemical linkage (SCL), for a systematic pruning of metabolic graphs. By analyzing the metabolic graph of Escherichia coli, we show that thresholding SCL is powerful in selecting the conventional pathways' connectivity out of the raw network connectivity when the network is restricted to the reactions collected from these pathways. Further, we argue that the root of ambiguity in pruning metabolic graphs is in the continuity of the amount of chemical content that can be conserved in reaction transformation patterns. Finally, we demonstrate how biochemical pathways can be inferred efficiently if the search procedure is guided by SCL.
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