Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

dc.citation.issueNumber1en_US
dc.citation.volumeNumber19en_US
dc.contributor.authorOlgun, G.en_US
dc.contributor.authorSahin, O.en_US
dc.contributor.authorTastan, O.en_US
dc.date.accessioned2019-02-21T16:07:22Z
dc.date.available2019-02-21T16:07:22Z
dc.date.issued2018en_US
dc.departmentDepartment of Computer Engineeringen_US
dc.departmentDepartment of Molecular Biology and Geneticsen_US
dc.description.abstractBackground: Long non-coding RNAs (lncRNAs) can indirectly regulate mRNAs expression levels by sequestering microRNAs (miRNAs), and act as competing endogenous RNAs (ceRNAs) or as sponges. Previous studies identified lncRNA-mediated sponge interactions in various cancers including the breast cancer. However, breast cancer subtypes are quite distinct in terms of their molecular profiles; therefore, ceRNAs are expected to be subtype-specific as well. Results: To find lncRNA-mediated ceRNA interactions in breast cancer subtypes, we develop an integrative approach. We conduct partial correlation analysis and kernel independence tests on patient gene expression profiles and further refine the candidate interactions with miRNA target information. We find that although there are sponges common to multiple subtypes, there are also distinct subtype-specific interactions. Functional enrichment of mRNAs that participate in these interactions highlights distinct biological processes for different subtypes. Interestingly, some of the ceRNAs also reside in close proximity in the genome; for example, those involving HOX genes, HOTAIR, miR-196a-1 and miR-196a-2. We also discover subtype-specific sponge interactions with high prognostic potential. We found that patients differ significantly in their survival distributions if they are group based on the expression patterns of specific ceRNA interactions. However, it is not the case if the expression of individual RNAs participating in ceRNA is used. Conclusion: These results can help shed light on subtype-specific mechanisms of breast cancer, and the methodology developed herein can help uncover sponges in other diseases.
dc.description.provenanceMade available in DSpace on 2019-02-21T16:07:22Z (GMT). No. of bitstreams: 1 Bilkent-research-paper.pdf: 222869 bytes, checksum: 842af2b9bd649e7f548593affdbafbb3 (MD5) Previous issue date: 2018en
dc.description.sponsorshipO.T. acknowledges support from Bilim Akademisi - The Science Academy, Turkey under the BAGEP program. This work is in part supported by TUBITAK-The Scientific and Technological Council of Turkey with grant number 214S364(O.S.).
dc.identifier.doi10.1186/s12864-018-5006-1en_US
dc.identifier.eissn1471-2164en_US
dc.identifier.urihttp://hdl.handle.net/11693/50360en_US
dc.language.isoEnglishen_US
dc.publisherBioMed Centralen_US
dc.relation.isversionofhttps://doi.org/10.1186/s12864-018-5006-1
dc.relation.project214S364
dc.rightsinfo:eu-repo/semantics/openAccess
dc.source.titleBMC Genomicsen_US
dc.subjectCeRNA interactionsen_US
dc.subjectKernel conditional independence testen_US
dc.subjectLncRNAen_US
dc.subjectLncRNA mediated spongesen_US
dc.subjectMiRNAen_US
dc.subjectNoncoding RNAen_US
dc.subjectPartial correlation analysisen_US
dc.titleDiscovering lncRNA mediated sponge interactions in breast cancer molecular subtypesen_US
dc.typeArticleen_US

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