Identification of functional differences in metabolic networks using comparative genomics and constraint-based models.

ABSTRACT: Genome-scale network reconstructions are useful tools for understanding cellular metabolism, and comparisons of such reconstructions can provide insight into metabolic differences between organisms. Recent efforts toward comparing genome-scale models have focused primarily on aligning metabolic networks at the reaction level and then looking at differences and similarities in reaction and gene content. However, these reaction comparison approaches are time-consuming and do not identify the effect network differences have on the functional states of the network. We have developed a bilevel mixed-integer programming approach, CONGA, to identify functional differences between metabolic networks by comparing network reconstructions aligned at the gene level. We first identify orthologous genes

SUBMITTER: Hamilton JJ 

PROVIDER: S-EPMC3359066 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature