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ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling
KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-6428-5936
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2018 (English)In: Frontiers in Physiology, ISSN 1664-042X, E-ISSN 1664-042X, Vol. 9, article id 1355Article in journal (Refereed) Published
Abstract [en]

Genome-scale metabolic models (GEMs) are comprehensive descriptions of cell metabolism and have been extensively used to understand biological responses in health and disease. One such application is in determining metabolic adaptation to the absence of a gene or reaction, i.e., essentiality analysis. However, current methods do not permit efficiently and accurately quantifying reaction/gene essentiality. Here, we present Essentiality Score Simulator (ESS), a tool for quantification of gene/reaction essentialities in GEMs. ESS quantifies and scores essentiality of each reaction/gene and their combinations based on the stoichiometric balance using synthetic lethal analysis. This method provides an option to weight metabolic models which currently rely mostly on topologic parameters, and is potentially useful to investigate the metabolic pathway differences between different organisms, cells, tissues, and/or diseases. We benchmarked the proposed method against multiple network topology parameters, and observed that our method displayed higher accuracy based on experimental evidence. In addition, we demonstrated its application in the wild-type and ldh knock-out E. coli core model, as well as two human cell lines, and revealed the changes of essentiality in metabolic pathways based on the reactions essentiality score. ESS is available without any limitation at https://sourceforge.net/projects/essentiality-score-simulator.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2018. Vol. 9, article id 1355
Keywords [en]
constraint-based modeling, gene essentiality, genome-scale metabolic models, reaction essentiality, systems biology
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-236008DOI: 10.3389/fphys.2018.01355ISI: 000445930500001OAI: oai:DiVA.org:kth-236008DiVA, id: diva2:1256095
Funder
Knut and Alice Wallenberg Foundation
Note

QC 20181016

Available from: 2018-10-16 Created: 2018-10-16 Last updated: 2019-04-26Bibliographically approved

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Bidkhori, GholamrezaBenfeitas, RuiLee, SunjaeArif, MuhammadMardinoglu, Adil

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