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dc.contributor.authorAbu-Jamous, Basel
dc.contributor.authorFa, Rui
dc.contributor.authorRoberts, David
dc.contributor.authorNandi, Asoke
dc.date.accessioned2014-02-11T10:37:56Z
dc.date.available2014-02-11T10:37:56Z
dc.date.issued2013
dc.identifier.citationAbu-Jamous, B., Fa, R., Roberts, D., & Nandi, A. (2013). Yeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experiments. <i>Journal of the Royal Society Interface</i>, <i>10</i>(81), 20120990. <a href="https://doi.org/10.1098/rsif.2012.0990" target="_blank">https://doi.org/10.1098/rsif.2012.0990</a>
dc.identifier.otherCONVID_23137463
dc.identifier.otherTUTKAID_60082
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/42937
dc.description.abstractThe binarization of consensus partition matrices (Bi-CoPaM) method has, among its unique features, the ability to perform ensemble clustering over the same set of genes from multiple microarray datasets by using various clustering methods in order to generate tunable tight clusters. Therefore, we have used the Bi-CoPaM method to the most synchronized 500 cell-cycle-regulated yeast genes from different microarray datasets to produce four tight, specific and exclusive clusters of co-expressed genes. We found 19 genes formed the tightest of the four clusters and this included the gene CMR1/YDL156W, which was an uncharacterized gene at the time of our investigations. Two very recent proteomic and biochemical studies have independently revealed many facets of CMR1 protein, although the precise functions of the protein remain to be elucidated. Our computational results complement these biological results and add more evidence to their recent findings of CMR1 as potentially participating in many of the DNA-metabolism processes such as replication, repair and transcription. Interestingly, our results demonstrate the close co-expressions of CMR1 and the replication protein A (RPA), the cohesion complex and the DNA polymerases α, δ and ɛ, as well as suggest functional relationships between CMR1 and the respective proteins. In addition, the analysis provides further substantial evidence that the expression of the CMR1 gene could be regulated by the MBF complex. In summary, the application of a novel analytic technique in large biological datasets has provided supporting evidence for a gene of previously unknown function, further hypotheses to test, and a more general demonstration of the value of sophisticated methods to explore new large datasets now so readily generated in biological experiments.fi
dc.language.isoeng
dc.publisherThe Royal Society
dc.relation.ispartofseriesJournal of the Royal Society Interface
dc.subject.otherCMR1/YDL156W
dc.subject.otherG1/S transition
dc.subject.otherDNA replication
dc.subject.otherDNA repair
dc.subject.otherbinarization of consensus partition matrix
dc.titleYeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experiments
dc.typearticle
dc.identifier.urnURN:NBN:fi:jyu-201402111216
dc.contributor.laitosTietotekniikan laitosfi
dc.contributor.laitosDepartment of Mathematical Information Technologyen
dc.contributor.oppiaineTietotekniikkafi
dc.contributor.oppiaineMathematical Information Technologyen
dc.type.urihttp://purl.org/eprint/type/JournalArticle
dc.date.updated2014-02-11T04:30:03Z
dc.type.coarhttp://purl.org/coar/resource_type/c_2df8fbb1
dc.description.reviewstatuspeerReviewed
dc.format.pagerange20120990
dc.relation.issn1742-5689
dc.relation.numberinseries81
dc.relation.volume10
dc.type.versionpublishedVersion
dc.rights.copyright© 2013 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited.
dc.rights.accesslevelopenAccessfi
dc.rights.urlhttp://creativecommons.org/licenses/by/3.0/
dc.relation.doi10.1098/rsif.2012.0990
dc.type.okmA1


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© 2013 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited.
Except where otherwise noted, this item's license is described as © 2013 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited.