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dc.contributor.authorGaire, RK
dc.contributor.authorBailey, J
dc.contributor.authorBearfoot, J
dc.contributor.authorCampbell, IG
dc.contributor.authorStuckey, PJ
dc.contributor.authorHaviv, I
dc.date.available2014-05-22T04:11:40Z
dc.date.issued2010-01-15
dc.identifierpii: btp654
dc.identifier.citationGaire, R. K., Bailey, J., Bearfoot, J., Campbell, I. G., Stuckey, P. J. & Haviv, I. (2010). MIRAGAA-a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer. BIOINFORMATICS, 26 (2), pp.161-167. https://doi.org/10.1093/bioinformatics/btp654.
dc.identifier.issn1367-4803
dc.identifier.urihttp://hdl.handle.net/11343/31772
dc.description.abstractMOTIVATION: Cancer evolves through microevolution where random lesions that provide the biggest advantage to cancer stand out in their frequent occurrence in multiple samples. At the same time, a gene function can be changed by aberration of the corresponding gene or modification of microRNA (miRNA) expression, which attenuates the gene. In a large number of cancer samples, these two mechanisms might be distributed in a coordinated and almost mutually exclusive manner. Understanding this coordination may assist in identifying changes which significantly produce the same functional impact on cancer phenotype, and further identify genes that are universally required for cancer. Present methodologies for finding aberrations usually analyze single datasets, which cannot identify such pairs of coordinating genes and miRNAs. RESULTS: We have developed MIRAGAA, a statistical approach, to assess the coordinated changes of genome copy numbers and miRNA expression. We have evaluated MIRAGAA on The Cancer Genome Atlas (TCGA) Glioblastoma Multiforme datasets. In these datasets, a number of genome regions coordinating with different miRNAs are identified. Although well known for their biological significance, these genes and miRNAs would be left undetected for being less significant if the two datasets were analyzed individually. AVAILABILITY AND IMPLEMENTATION: The source code, implemented in R and java, is available from our project web site at http://www.csse.unimelb.edu.au/~rgaire/MIRAGAA/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
dc.languageEnglish
dc.publisherOXFORD UNIV PRESS
dc.subjectInformation Systems
dc.titleMIRAGAA-a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer
dc.typeJournal Article
dc.identifier.doi10.1093/bioinformatics/btp654
melbourne.peerreviewPeer Reviewed
melbourne.affiliationThe University of Melbourne
melbourne.affiliation.departmentComputer Science and Software Engineering
melbourne.source.titleBIOINFORMATICS
melbourne.source.volume26
melbourne.source.issue2
melbourne.source.pages161-167
dc.research.codefor0806
dc.description.pagestart161
melbourne.publicationid143433
melbourne.elementsid321945
melbourne.contributor.authorBailey, James
melbourne.contributor.authorCampbell, Ian
melbourne.contributor.authorStuckey, Peter
melbourne.contributor.authorHaviv, Izhak
melbourne.contributor.authorGAIRE, RAJ
dc.identifier.eissn1367-4811
melbourne.accessrightsThis item is currently not available from this repository


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