Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants

Noorlin Mohd Ali; Ryo Tsuboi; Yuta Matsumoto; Daisuke Koishi; Kentaro Inoue; Kazuhiro Maeda; Hiroyuki Kurata

doi:10.1016/j.jbiosc.2015.12.001

Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants

J Biosci Bioeng. 2016 Jul;122(1):111-6. doi: 10.1016/j.jbiosc.2015.12.001. Epub 2016 Jan 6.

Authors

Noorlin Mohd Ali¹, Ryo Tsuboi¹, Yuta Matsumoto¹, Daisuke Koishi¹, Kentaro Inoue¹, Kazuhiro Maeda², Hiroyuki Kurata³

Affiliations

¹ Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
² Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
³ Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan. Electronic address: kurata@bio.kyutech.ac.jp.

PMID: 26777238
DOI: 10.1016/j.jbiosc.2015.12.001

Abstract

Computational analysis of metabolic fluxes is essential in understanding the structure and function of a metabolic network and in rationally designing genetically modified mutants for an engineering purpose. We had presented the genetic modification flux (GMF) that predicts the flux distribution of a broad range of genetically modified mutants. To enhance the feasibility and usability of GMF, we have developed a web application with a metabolic network database to predict a flux distribution of genetically modified mutants. One hundred and twelve data sets of Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Chinese hamster ovary were registered as standard models.

Keywords: Elementary mode; Flux mutant prediction; Genetic modification; Genetic mutant database; Metabolic flux analysis; Metabolic flux estimation; Metabolic network data; Systems biology.

MeSH terms

Animals
CHO Cells
Corynebacterium glutamicum / genetics
Corynebacterium glutamicum / metabolism
Cricetinae
Cricetulus / genetics
Databases, Factual*
Datasets as Topic
Escherichia coli / genetics
Escherichia coli / metabolism
Metabolic Engineering
Metabolic Flux Analysis*
Metabolic Networks and Pathways / genetics*
Models, Biological*
Mutation*
Saccharomyces cerevisiae / genetics
Saccharomyces cerevisiae / metabolism