TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.

ABSTRACT:

Background

Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR) relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model.

Results

We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into

SUBMITTER: Jensen PA 

PROVIDER: S-EPMC3224351 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature