Reproducible Cancer Biomarker Discovery in SELDI-TOF MS Using Different Pre-Processing Algorithms 英文参考文献.docVIP

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Reproducible Cancer Biomarker Discovery in SELDI-TOF MS Using Different Pre-Processing Algorithms 英文参考文献.doc

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Reproducible Cancer Biomarker Discovery in SELDI-TOF MS Using Different Pre-Processing Algorithms 英文参考文献

ReproducibleCancerBiomarkerDiscoveryinSELDI-TOF MSUsingDifferentPre-ProcessingAlgorithms JinfengZou1,GuiniHong1,XinwuGuo2,LinZhang1,ChenYao1,JingWang1,ZhengGuo1,2* 1BioinformaticsCentre,SchoolofLifeScience,UniversityofElectronicScienceandTechnologyofChina,Chengdu,People’sRepublicofChina,2CollegeofBioinformatics ScienceandTechnology,HarbinMedicalUniversity,Harbin,People’sRepublicofChina Abstract Background:Therehasbeenmuchinterestindifferentiatingdiseasedandnormalsamplesusingbiomarkersderivedfrom mass spectrometry (MS) studies. However, biomarker identification for specific diseases has been hindered by irreproducibility. Specifically,apeakprofileextractedfromadatasetforbiomarkeridentificationdependsonadatapre- processingalgorithm.Untilnow,nowidelyacceptedagreementhasbeenreached. Results:Inthispaper,weinvestigatedtheconsistencyofbiomarkeridentificationusingdifferentiallyexpressed(DE)peaks frompeakprofilesproducedbythreewidelyusedaveragespectrum-dependentpre-processingalgorithmsbasedonSELDI- TOFMSdataforprostateandbreastcancers.OurresultsrevealedtwoimportantfactorsthataffecttheconsistencyofDE peakidentificationusingdifferentalgorithms.OnefactoristhatsomeDEpeaksselectedfromonepeakprofilewerenot detectedaspeaksinotherprofiles,andthesecondfactoristhatthestatisticalpowerofidentifyingDEpeaksinlargepeak profileswithmanypeaksmaybelowduetothelargescaleofthetestsandsmallnumberofsamples.Furthermore,we demonstratedthattheDEpeakdetectionpowerinlargeprofilescouldbeimprovedbythestratifiedfalsediscoveryrate (FDR)controlapproachandthatthereproducibilityofDEpeakdetectioncouldtherebybeincreased. Conclusions:Comparingandevaluatingpre-processingalgorithmsintermsofreproducibilitycanelucidatetherelationship amongdifferentalgorithmsandalsohelpinselectingapre-processingalgorithm.TheDEpeaksselectedfromsmallpeak profileswithfewpeaksforadatasettendtobereproduciblydetectedinlargepeakprofiles,whichsuggeststhatasuitable pre-processingalgorithmshouldbeabletoproducepeakssufficientforidentifyingu