Metabolic model refinement using phenotypic microarray data

Pratish Gawand; Laurence Yang; William R Cluett; Radhakrishnan Mahadevan

doi:10.1007/978-1-62703-299-5_3

Metabolic model refinement using phenotypic microarray data

Methods Mol Biol. 2013:985:47-59. doi: 10.1007/978-1-62703-299-5_3.

Authors

Pratish Gawand¹, Laurence Yang, William R Cluett, Radhakrishnan Mahadevan

Affiliation

¹ Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.

PMID: 23417798
DOI: 10.1007/978-1-62703-299-5_3

Abstract

Phenotypic microarray (PM) is a standardized, high-throughput technology for profiling phenotypes of microorganisms, which allows for characterization on around 2,000 different media conditions. The data generated using PM can be incorporated into genome-scale metabolic models to improve their predictive capability. In addition, a comparison of phenotypic profiles of wild-type and gene knockout mutants can give essential information about gene functions of unknown genes. In this chapter, we present a protocol to refine preconstructed metabolic models using the PM data. Both manual refinement and algorithmic approaches for integrating the PM data into metabolic models have been discussed.

MeSH terms

Bacteria / genetics
Bacteria / metabolism*
Computer Simulation
Decision Trees
Metabolic Networks and Pathways / genetics*
Microarray Analysis
Models, Biological*
Molecular Sequence Annotation / methods
Phenotype