{"database":"biostudies-other","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Lucian Smith"],"journal":["PeerJ PrePrints"],"species":["Saccharomyces cerevisiae"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/MODEL1311290001"],"repository":["biostudies-other"],"additional_accession":["10.7287/peerj.preprints.146v2"],"pubmed_authors":["Lucian Smith","Kieran Smallbone"]},"is_claimable":false,"name":"Messiha2013 - combined glycolysis and pentose phosphate pathway model","description":"

Messiha2013 - combined glycolysis and pentose phosphate pathway model

BIOMD0000000502 and MODEL1303260018 are combined to examine the response to oxidative stress.

This model is described in the article:

Enzyme characterisation and kinetic modelling of pentose phosphate pathway in yeast.

Hanan L. Messiha, Edward Kent, Naglis Malys, Kathleen M. Carroll, Pedro Mendes, Kieran Smallbone

PeerJ PrePrints 1:e146v2

Abstract:

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows for the predicting changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis one to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardized enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network models by merging smaller pathway models.

This model is hosted on BioModels Database and identifiedby: BIOMD0000000503 .

To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resourcefor published quantitative kinetic models .

To the extent possible under law, all copyright and related orneighbouring rights to this encoded model have been dedicated to the publicdomain worldwide. Please refer to CC0 Public Domain Dedication for more information.

","dates":{"release":"2013-11-29T00:00:00Z","modification":"2025-07-15T10:02:47.059Z","creation":"2025-03-29T13:20:20.679Z"},"accession":"MODEL1311290001","cross_references":{"sgd":["S000004818","S000001949","S000001206","S000000036","S000001543","S000004711","S000003424","S000002457","S000001226","S000004124","S000004346","S000003472","S000002481","S000003275","S000002180","S000000605","S000001518","S000001217","S000000545","S000001635","S000000864","S000003319","S000000400","S000001610","S000003657","S000001315","S000005621","S000003222","S000003486","S000003588","S000003488","S000005446","S000006278","S000000330","S000005420","S000004034","S000005185"],"ec-code":["2.7.1.11","2.4.1.15","3.1.1.31","5.3.1.9","1.1.1.94","5.3.1.6","3.1.3.12","5.3.1.1","2.7.1.1","2.7.4.3","2.7.2.3","5.4.2.2","5.4.2.1","2.7.7.9","1.1.1.1","1.1.1.44","1.1.1.49","3.1.3.21","4.1.2.13","2.2.1.1","5.1.3.1","2.2.1.2","4.1.1.1","4.2.1.11","1.2.1.12","2.7.1.40"],"biomodels___db":["MODEL1303260018","BIOMD0000000502","BIOMD0000000503"],"kegg___compound":["C00002","C01236","C00022","C00020","C00042","C03736","C00084","C00008","C00668","C00469","C00006","C00005","C05378","C00665","C00345","C00004","C00003","C00199","C00111","C00231","C00197","C00031","C00074","C00093","C05382","C01083","C00118","C00116","C00236","C05345","C00279","C00631"],"chebi":["CHEBI:58759","CHEBI:28602","CHEBI:46398","CHEBI:30089","CHEBI:29052","CHEBI:4167","CHEBI:15846","CHEBI:16027","CHEBI:17754","CHEBI:16001","CHEBI:18189","CHEBI:16761","CHEBI:17794","CHEBI:18066","CHEBI:16084","CHEBI:30031","CHEBI:18021","CHEBI:58121","CHEBI:18283","CHEBI:57737","CHEBI:57955","CHEBI:16908","CHEBI:58349","CHEBI:28013","CHEBI:16108","CHEBI:15978","CHEBI:17835","CHEBI:17659","CHEBI:15422","CHEBI:16236","CHEBI:17665","CHEBI:16897","CHEBI:16551","CHEBI:16077","CHEBI:15343","CHEBI:15361","CHEBI:57783","CHEBI:57483"],"mamo":["MAMO_0000046"],"go":["GO:0016887","GO:0006098","GO:0006096","GO:0004022","GO:0004396","GO:0005576","GO:0006105","GO:0004332","GO:0004365","GO:0003872","GO:0004634","GO:0004017","GO:0004347","GO:0004743","GO:0004737","GO:0004618","GO:0004807","GO:0005829","GO:0004619","GO:0015758"],"taxonomy":["4932"],"kegg___genes":["sce:YHR183W","sce:YGR043C","sce:YPR074C","sce:YOR095C","sce:YNL241C","sce:YLR354C","sce:YGR256W","sce:YJL121C","sce:YHR163W"],"kegg___reaction":["R01518","R02848","R00200","R01015","R00841","R01512","R00754","R00127","R00842","R00756","R00658","R00636","R01061","R01068","R00771"],"uniprot":["Q12189","P26263","P38720","P53228","P32861","P14540","P16862","P16861","P00925","P41277","P46969","P00549","P00924","P00942","P17709","P41911","P40106","A5YWB0","P06169","P00560","P31688","P12709","P00360","P11412","P38858","P04806","P53319","P15019","P04807","P16467","P33401","P37012","Q00764","P00359","P00950","P23254","P00330"],"doi":["10.7287/peerj.preprints.146v2"]}}