Experimental Comparison and Evaluation of the Affymetrix Exon and U133Plus2 GeneChip Arrays 英文参考文献.docVIP

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Experimental Comparison and Evaluation of the Affymetrix Exon and U133Plus2 GeneChip Arrays 英文参考文献.doc

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Experimental Comparison and Evaluation of the Affymetrix Exon and U133Plus2 GeneChip Arrays 英文参考文献

ExperimentalComparisonandEvaluationofthe AffymetrixExonandU133Plus2GeneChipArrays DianaAbdueva*,MicheleR.Wing,BettySchaub,TimothyJ.Triche Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, LosAngeles,California,UnitedStatesofAmerica Background.Affymetrixexonarraysofferscientiststheonlysolutionforexon-levelexpressionprofilingatthewhole-genome scaleonasinglearray.Thesearraysfeatureanewchipdesignwithnomismatchprobesandaradicallynewrandomprimed protocol to generate sense DNA targets along the entire length of the transcript. In addition to these changes, a limited numberofvalidatingexperimentsandvirtuallynoexperimentaldatatorigorouslyaddressthecomparabilityofall-exonarrays with conventional 39-arrays result in a natural reluctance to replace conventional expression arrays with the new all-exon platform.Methodology.UsingcommerciallyavailableAffymetrixarrays,weassesstheperformanceoftheHumanExon1.0ST (HuEx)andU133Plus2.0(U133Plus2)platformsdirectlythroughaseriesof‘spike-in’hybridizationscontaining25transcripts inthepresenceofafixedeukaryoticbackground.Specifically,wecomparethemeasuresofexpressionforHuExandU133Plus2 arraystoevaluatetheprecisionofthesemeasuresaswellasthespecificityandsensitivityofthemeasures’abilitytodetect differential expression. Significance. This study presents an experimental comparison and systematic cross-validation of Affymetrix exon arrays and establishes high comparability of expression changes and probe performance characteristics between Affymetrix conventional and exon arrays. In addition, this study offers a reliable benchmark data set for the comparisonofcompetingexonexpressionmeasures,theselectionofmethodssuitableformappingexonarraymeasuresto the wealth ofpreviously generated microarray data, as well as the development ofmore advanced methodsfor exon- and transcript-levelexpressionsummarization. Citation: AbduevaD,WingMR,SchaubB,TricheTJ(2007)Experime