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ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling
KTH, Centra, Science for Life Laboratory, SciLifeLab.
KTH, Centra, Science for Life Laboratory, SciLifeLab.
KTH, Centra, Science for Life Laboratory, SciLifeLab.
KTH, Centra, Science for Life Laboratory, SciLifeLab.ORCID-id: 0000-0002-6428-5936
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2018 (Engelska)Ingår i: Frontiers in Physiology, ISSN 1664-042X, E-ISSN 1664-042X, Vol. 9, artikel-id 1355Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
Frontiers Media S.A., 2018. Vol. 9, artikel-id 1355
Nyckelord [en]
constraint-based modeling, gene essentiality, genome-scale metabolic models, reaction essentiality, systems biology
Nationell ämneskategori
Bioinformatik (beräkningsbiologi)
Identifikatorer
URN: urn:nbn:se:kth:diva-236008DOI: 10.3389/fphys.2018.01355ISI: 000445930500001OAI: oai:DiVA.org:kth-236008DiVA, id: diva2:1256095
Forskningsfinansiär
Knut och Alice Wallenbergs Stiftelse
Anmärkning

QC 20181016

Tillgänglig från: 2018-10-16 Skapad: 2018-10-16 Senast uppdaterad: 2020-01-10Bibliografiskt granskad

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Bidkhori, GholamrezaBenfeitas, RuiLee, SunjaeArif, MuhammadMardinoglu, Adil

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Zhang, ChengBidkhori, GholamrezaBenfeitas, RuiLee, SunjaeArif, MuhammadUhlen, MathiasMardinoglu, Adil
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Science for Life Laboratory, SciLifeLabSystembiologi
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