A shiny application for pancan survival analysis with paralog/miRNA pairs and in vitro validation of miRNA synergism in liver cancer

buir.advisorKarakayalı, Özlen Konu
dc.contributor.authorTombaz, Melike
dc.date.accessioned2022-09-23T08:00:26Z
dc.date.available2022-09-23T08:00:26Z
dc.date.copyright2022-09
dc.date.issued2022-09
dc.date.submitted2022-09-21
dc.departmentDepartment of Molecular Biology and Geneticsen_US
dc.descriptionCataloged from PDF version of article.en_US
dc.descriptionThesis (Master's): Bilkent University, Department of Molecular Biology and Genetics, İhsan Doğramacı Bilkent University, 2022.en_US
dc.descriptionIncludes bibliographical references (leaves 82-92).en_US
dc.description.abstractEmerging cancer survival tools can predict risk of disease and identify prognostic biomarkers. Multivariable Cox proportional hazards models with mRNA and microRNAs (miRNAs) expression can differentiate survival outcomes. Previous studies showed that genes that belong to the same pathways/families may act independently, and in a cancer-specific manner. In this thesis, cancer-dependent hazard ratios of paralog genes and sense-antisense strands of miRNAs were tested for TCGA PANCAN. The results were presented in a R/Shiny web application that provides gene-by-survival networks. The gene-by-survival network approach also was applied to the plasma membrane-endoplasmic reticulum (PM-ER) calcium channel geneset. Among paralogs, cancer-specific prognostic signatures and functional compartmentalization were observed. Some cancers like UVM, MESO emerged as hub cancers for PM-ER signalling. Further the proposed gene-by-survival network approach has been extended for miRNA-mRNA triplets that may act in synergy in hepatocellular carcinoma (HCC). Next, the effects of synergistic miRNA pairs provided by miRCoop algorithm were tested on cell viability and target gene expression for selected triplets. The results have revealed that the combinatorial miRNA treatments show promising results as RNAi therapeutics yet future studies with different doses and triplets are needed.en_US
dc.description.degreeM.S.en_US
dc.description.statementofresponsibilityby Melike Tombazen_US
dc.embargo.release2023-03-16
dc.format.extentxv, 97 leaves : illustrations (some color), charts, graphics ; 30 cm.en_US
dc.identifier.itemidB161356
dc.identifier.urihttp://hdl.handle.net/11693/110585
dc.language.isoEnglishen_US
dc.publisherBilkent Universityen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectSurvivalen_US
dc.subjectmiRNAsen_US
dc.subjectParalogsen_US
dc.subjectTCGA-PANCANen_US
dc.subjectPrognosisen_US
dc.subjectGene networken_US
dc.titleA shiny application for pancan survival analysis with paralog/miRNA pairs and in vitro validation of miRNA synergism in liver canceren_US
dc.title.alternativeParalog/miRNA çiftleri ile pancan sağkalım analiz shiny aplikasyonu ve karaciğer kanserinde miRNA sinerjizminin in vitro doğrulanmasıen_US
dc.typeThesisen_US
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