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dc.contributor.authorLi, Qiyuan
dc.contributor.authorBirkbak, Nicolai Juul
dc.contributor.authorGyorffy, Balazs
dc.contributor.authorSzallasi, Zoltan
dc.contributor.authorEklund, Aron C
dc.date.accessioned2013-02-14T18:59:10Z
dc.date.issued2011
dc.identifier.citationLi, Qiyuan, Nicolai J. Birkbak, Balazs Gyorffy, Zoltan Szallasi, and Aron C. Eklund. 2011. Jetset: Selecting the optimal microarray probe set to represent a gene. BMC Bioinformatics 12:474.en_US
dc.identifier.issn1471-2105en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:10295333
dc.description.abstractBackground: Interpretation of gene expression microarrays requires a mapping from probe set to gene. On many Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets, which may deliver inconsistent or even contradictory measurements. Therefore, obtaining an unambiguous expression estimate of a pre-specified gene can be a nontrivial but essential task. Results: We developed scoring methods to assess each probe set for specificity, splice isoform coverage, and robustness against transcript degradation. We used these scores to select a single representative probe set for each gene, thus creating a simple one-to-one mapping between gene and probe set. To test this method, we evaluated concordance between protein measurements and gene expression values, and between sets of genes whose expression is known to be correlated. For both test cases, we identified genes that were nominally detected by multiple probe sets, and we found that the probe set chosen by our method showed stronger concordance. Conclusions: This method provides a simple, unambiguous mapping to allow assessment of the expression levels of specific genes of interest.en_US
dc.language.isoen_USen_US
dc.publisherBioMed Centralen_US
dc.relation.isversionofdoi:10.1186/1471-2105-12-474en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266307/pdf/en_US
dash.licenseLAA
dc.titleJetset: Selecting the Optimal Microarray Probe Set to Represent a Geneen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalBMC Bioinformaticsen_US
dash.depositing.authorSzallasi, Zoltan
dc.date.available2013-02-14T18:59:10Z
dc.identifier.doi10.1186/1471-2105-12-474*
dash.contributor.affiliatedLi, Qiyuan
dash.contributor.affiliatedSzallasi, Zoltan
dash.contributor.affiliatedBirkbak, N


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