The strength of chemical linkage as a criterion for pruning metabolic graphs.

ABSTRACT:

Motivation

A 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.

Results

We 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'

SUBMITTER: Zhou W 

PROVIDER: S-EPMC3129522 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature