TY - GEN
T1 - Identifying minimal genomes and essential genes in metabolic model using flux balance analysis
AU - Salleh, Abdul Hakim Mohamed
AU - Mohamad, Mohd Saberi
AU - Deris, Safaai
AU - Illias, Rosli Md
PY - 2013
Y1 - 2013
N2 - With the advancement in metabolic engineering technologies, reconstruction the genome of a host organism to achieve desired phenotypes for example, to optimize the production of metabolites can be made. However, due to the complexity and size of the genome scale metabolic network, significant components tend to be invisible. This research utilizes Flux Balance Analysis (FBA) to search the essential genes and obtain minimal functional genome. Different from traditional approaches, we identify essential genes by using single gene deletions and then we identify the significant pathway for the metabolite production using gene expression data. The experiment is conducted using genome scale metabolic model of Saccharomyces Cerevisiae for L-phenylalanine production. The result has shown the reliability of this approach to find essential genes for metabolites productions, reduce genome size and identify production pathway that can further optimize the production yield and can be applied in solving other genetic engineering problems.
AB - With the advancement in metabolic engineering technologies, reconstruction the genome of a host organism to achieve desired phenotypes for example, to optimize the production of metabolites can be made. However, due to the complexity and size of the genome scale metabolic network, significant components tend to be invisible. This research utilizes Flux Balance Analysis (FBA) to search the essential genes and obtain minimal functional genome. Different from traditional approaches, we identify essential genes by using single gene deletions and then we identify the significant pathway for the metabolite production using gene expression data. The experiment is conducted using genome scale metabolic model of Saccharomyces Cerevisiae for L-phenylalanine production. The result has shown the reliability of this approach to find essential genes for metabolites productions, reduce genome size and identify production pathway that can further optimize the production yield and can be applied in solving other genetic engineering problems.
KW - essential genes
KW - flux balance analysis
KW - Metabolic engineering
KW - metabolites productions
KW - minimal genome
UR - http://www.scopus.com/inward/record.url?scp=84874613148&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84874613148&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-36546-1_43
DO - 10.1007/978-3-642-36546-1_43
M3 - Conference contribution
AN - SCOPUS:84874613148
SN - 9783642365454
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 414
EP - 423
BT - Intelligent Information and Database Systems - 5th Asian Conference, ACIIDS 2013, Proceedings
T2 - 5th Asian Conference on Intelligent Information and Database Systems, ACIIDS 2013
Y2 - 18 March 2013 through 20 March 2013
ER -