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dc.contributor.authorHo, Yen-Yien_US
dc.contributor.authorCope, Leslie M.en_US
dc.contributor.authorParmigiani, Giovannien_US
dc.date.accessioned2014-04-11T14:11:29Z
dc.date.issued2014en_US
dc.identifier.citationHo, Yen-Yi, Leslie M. Cope, and Giovanni Parmigiani. 2014. “Modular network construction using eQTL data: an analysis of computational costs and benefits.” Frontiers in Genetics 5 (1): 40. doi:10.3389/fgene.2014.00040. http://dx.doi.org/10.3389/fgene.2014.00040.en
dc.identifier.issn1664-8021en
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:12064408
dc.description.abstractBackground: In this paper, we consider analytic methods for the integrated analysis of genomic DNA variation and mRNA expression (also named as eQTL data), to discover genetic networks that are associated with a complex trait of interest. Our focus is the systematic evaluation of the trade-off between network size and network search efficiency in the construction of these networks. Results: We developed a modular approach to network construction, building from smaller networks to larger ones, thereby reducing the search space while including more variables in the analysis. The goal is achieving a lower computational cost while maintaining high confidence in the resulting networks. As demonstrated in our simulation results, networks built in this way have low node/edge false discovery rate (FDR) and high edge sensitivity comparing to greedy search. We further demonstrate our method in a data set of cellular responses to two chemotherapeutic agents: docetaxel and 5-fluorouracil (5-FU), and identify biologically plausible networks that might describe resistances to these drugs. Conclusion: In this study, we suggest that guided comprehensive searches for parsimonious networks should be considered as an alternative to greedy network searches.en
dc.language.isoen_USen
dc.publisherFrontiers Media S.A.en
dc.relation.isversionofdoi:10.3389/fgene.2014.00040en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3935177/pdf/en
dash.licenseLAAen_US
dc.subjectMethods Articleen
dc.subjectBayesian networksen
dc.subjectsearch algorithmen
dc.subjectnetwork variable selectionen
dc.subjecteQTLen
dc.subjectchemotherapy resistanceen
dc.titleModular network construction using eQTL data: an analysis of computational costs and benefitsen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalFrontiers in Geneticsen
dash.depositing.authorParmigiani, Giovannien_US
dc.date.available2014-04-11T14:11:29Z
dc.identifier.doi10.3389/fgene.2014.00040*
dash.contributor.affiliatedParmigiani, Giovanni


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