{"database":"biostudies-other","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["15"],"submitter":["Nicolas Le Novère"],"journal":["Genome research"],"pagination":["1421-1430"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/MODEL1507180066"],"repository":["biostudies-other"],"additional_accession":["16204195"],"pubmed_authors":["Nicolas Le Novère"]},"is_claimable":false,"name":"Kuepfer2005 - Genome-scale metabolic network of Saccharomyces cerevisiae (iLL672)","description":"<notes xmlns=\"http://www.sbml.org/sbml/level3/version1/core\">      <body xmlns=\"http://www.w3.org/1999/xhtml\">        <div class=\"dc:title\">Kuepfer2005 - Genome-scale metabolic networkof Saccharomyces cerevisiae (iLL672)</div><div class=\"dc:bibliographicCitation\">  <p>This model is described in the article:</p>  <div class=\"bibo:title\">    <a href=\"http://identifiers.org/pubmed/16204195\" title=\"Access to this publication\">Metabolic functions of    duplicate genes in Saccharomyces cerevisiae.</a>  </div>  <div class=\"bibo:authorList\">Kuepfer L, Sauer U, Blank LM.</div>  <div class=\"bibo:Journal\">Genome Res. 2005 Oct; 15(10):  1421-1430</div>  <p>Abstract:</p>  <div class=\"bibo:abstract\">    <p>The roles of duplicate genes and their contribution to the    phenomenon of enzyme dispensability are a central issue in    molecular and genome evolution. A comprehensive classification    of the mechanisms that may have led to their preservation,    however, is currently lacking. In a systems biology approach,    we classify here back-up, regulatory, and gene dosage functions    for the 105 duplicate gene families of Saccharomyces cerevisiae    metabolism. The key tool was the reconciled genome-scale    metabolic model iLL672, which was based on the older iFF708.    Computational predictions of all metabolic gene knockouts were    validated with the experimentally determined phenotypes of the    entire singleton yeast library of 4658 mutants under five    environmental conditions. iLL672 correctly identified 96%-98%    and 73%-80% of the viable and lethal singleton phenotypes,    respectively. Functional roles for each duplicate family were    identified by integrating the iLL672-predicted in silico    duplicate knockout phenotypes, genome-scale carbon-flux    distributions, singleton mutant phenotypes, and network    topology analysis. The results provide no evidence for a    particular dominant function that maintains duplicate genes in    the genome. In particular, the back-up function is not favored    by evolutionary selection because duplicates do not occur more    frequently in essential reactions than singleton genes. Instead    of a prevailing role, multigene-encoded enzymes cover different    functions. Thus, at least for metabolism, persistence of the    paralog fraction in the genome can be better explained with an    array of different, often overlapping functional roles.</p>  </div></div><div class=\"dc:publisher\">  <p>This model is hosted on   <a href=\"http://www.ebi.ac.uk/biomodels/\">BioModels Database</a>  and identified by:   <a href=\"http://identifiers.org/biomodels.db/MODEL1507180066\">MODEL1507180066</a>.</p>  <p>To cite BioModels Database, please use:   <a href=\"http://identifiers.org/pubmed/20587024\" title=\"Latest BioModels Database publication\">BioModels Database:  An enhanced, curated and annotated resource for published  quantitative kinetic models</a>.</p></div><div class=\"dc:license\">  <p>To the extent possible under law, all copyright and related or  neighbouring rights to this encoded model have been dedicated to  the public domain worldwide. Please refer to   <a href=\"http://creativecommons.org/publicdomain/zero/1.0/\" title=\"Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication\">CC0  Public Domain Dedication</a> for more information.</p></div></body>    </notes>","dates":{"release":"2015-07-18T00:00:00Z","modification":"2025-07-15T09:09:15.933Z","creation":"2025-03-30T22:03:07.087Z"},"accession":"MODEL1507180066","cross_references":{"pubmed":["16204195"],"mamo":["MAMO_0000009"],"unknown":["null"]}}