TY - JOUR
T1 - g2f as a Novel Tool to Find and Fill Gaps in Metabolic Networks
AU - Osorio, Daniel
AU - Botero, Kelly
AU - Velasco, Andrés Pinzón
AU - Mendoza-Mejía, Nicolás
AU - Rojas-Rodríguez, Felipe
AU - Barreto, George
AU - González, Janneth
N1 - Publisher Copyright:
© 2021, R Journal. All Rights Reserved.
PY - 2021
Y1 - 2021
N2 - During the building of a genome-scale metabolic model, there are several dead-end metabolites and substrates which cannot be imported, produced, nor used by any reaction incorporated in the network. The presence of these dead-end metabolites can block out the net flux of the objective function when it is evaluated through Flux Balance Analysis (FBA), and when it is not blocked, bias in the biological conclusions increase. In this aspect, the refinement to restore the connectivity of the network can be carried out manually or using computational algorithms. The g2f package was designed as a tool to find the gaps from dead-end metabolites and fill them from the stoichiometric reactions of a reference, filtering candidate reactions using a weighting function. Additionally, this algorithm allows downloading all the sets of gene-associated stoichiometric reactions for a specific organism from the KEGG database. Our package is compatible with both 4.0.0 and 3.6.0 R versions.
AB - During the building of a genome-scale metabolic model, there are several dead-end metabolites and substrates which cannot be imported, produced, nor used by any reaction incorporated in the network. The presence of these dead-end metabolites can block out the net flux of the objective function when it is evaluated through Flux Balance Analysis (FBA), and when it is not blocked, bias in the biological conclusions increase. In this aspect, the refinement to restore the connectivity of the network can be carried out manually or using computational algorithms. The g2f package was designed as a tool to find the gaps from dead-end metabolites and fill them from the stoichiometric reactions of a reference, filtering candidate reactions using a weighting function. Additionally, this algorithm allows downloading all the sets of gene-associated stoichiometric reactions for a specific organism from the KEGG database. Our package is compatible with both 4.0.0 and 3.6.0 R versions.
UR - http://www.scopus.com/inward/record.url?scp=85125371565&partnerID=8YFLogxK
U2 - 10.32614/RJ-2021-064
DO - 10.32614/RJ-2021-064
M3 - Article
AN - SCOPUS:85125371565
SN - 2073-4859
VL - 13
SP - 28
EP - 37
JO - R Journal
JF - R Journal
IS - 2
ER -