Development of a WEB application

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buir.advisorKonu, Özlen
dc.contributor.authorKaya, Koray Doğan
dc.date.accessioned2016-01-08T18:23:50Z
dc.date.available2016-01-08T18:23:50Z
dc.date.issued2011
dc.descriptionAnkara : The Department of Molecular Biology and Genetics and the Graduate School of Engineering and Science of Bilkent University, 2011.en_US
dc.descriptionThesis (Ph. D.) -- Bilkent University, 2011.en_US
dc.descriptionIncludes bibliographical references leaves 99-115.en_US
dc.description.abstractmicroRNAs, small non-coding RNA molecules with important roles in cellular machinery, target mRNAs for silencing by binding generally to their 3’ UTR sequences via partial base complementation. Thus, microRNAs with similar sequences also might exhibit expression and/or functional similarities. In this study, a modular tool, mESAdb (http://konulab.fen.bilkent.edu.tr/mirna/), was developed allowing for multivariate analysis of sequences and expression of microRNAs from multiple taxa. Its framework comprises PHP, JavaScript, packages in the R language, and a database storing mature microRNA sequences along with microRNA targets and selected expression data sets for human, mouse and zebrafish. mESAdb allows for: (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by a sequence motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HuGE Navigator, KEGG and GO. mESAdb also permits user specified dataset upload for these analyses. Herein, utility of mESAdb was illustrated using different datasets and case studies. First, it was shown that microRNAs carrying the embryonic stem cell specific seed sequence, ‘AAGTGC’, were able to discriminate between normal and tumor tissues from hepatocellular carcinoma patients using dataset GSE10694. Second, mRNA targets of a set of liver specific microRNAs were annotated with human diseases based on HuGE Navigator. Third, the similarity between mouse and human tissue specificity of a given set of microRNAs was demonstrated. Forth, CHRNA5 targeting microRNAs were associated with estrogen receptor status in breast cancer using dataset GSE15885. Finally, a related tool under development for mRNA arrays planned for integration with mESAdb was presented.en_US
dc.description.provenanceMade available in DSpace on 2016-01-08T18:23:50Z (GMT). No. of bitstreams: 1 0006447.pdf: 2368983 bytes, checksum: 65252b318c370b4c9c985843d752baa9 (MD5)en
dc.description.statementofresponsibilityKaya, Koray Doğanen_US
dc.format.extentxvii, 125 leaves, illustrationsen_US
dc.identifier.urihttp://hdl.handle.net/11693/15736
dc.language.isoEnglishen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectmESAdben_US
dc.subjectdatabaseen_US
dc.subjectRen_US
dc.subjectmicroRNAen_US
dc.subjectsequenceen_US
dc.subjectexpression data setsen_US
dc.subjectdata miningen_US
dc.subjectmultivariate analysisen_US
dc.subjectannotation databasesen_US
dc.subjectHuGEen_US
dc.subjectKEGGen_US
dc.subjectGOen_US
dc.subjectCHRNA5en_US
dc.subjectestrogen receptoren_US
dc.subjecthepatocellular carcinoma and breast canceren_US
dc.subject.lccQP623.5.S63 K39 2011en_US
dc.subject.lcshSmall interfering RNA.en_US
dc.subject.lcshCancer.en_US
dc.subject.lcshMicroRNAs--Genetics.en_US
dc.subject.lcshMicroRNAs--Therapeutic use.en_US
dc.subject.lcshGene expression regulation.en_US
dc.subject.lcshGene expression profiling.en_US
dc.titleDevelopment of a WEB applicationen_US
dc.typeThesisen_US
thesis.degree.disciplineMolecular Biology and Genetics
thesis.degree.grantorBilkent University
thesis.degree.levelDoctoral
thesis.degree.namePh.D. (Doctor of Philosophy)

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