MetaboAnalyst教学课件.pptx
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MetaboAnalyst教学课件.pptx
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MetaboAnalyst2.0&ROCCETJianguoXia,PhDUniversityofAlberta,CanadaDataAnalysis&BiomarkerDiscoveryOutlineIntroduction(updates)oftwofreewebapplicationMetaboAnalyst2.0ROCCETBackground&basicconceptsScreenshottutorialsLivedemo(ifwehavetime)6/25/2012Metabolomics20122MetabolomicDataAnalysis3MetaboAnalyst(www.metaboanalyst.ca)4OtherutilitiesTwo/multi-groupanalysisEnrichmentanalysisTime-seriesanalysisQualitycheckingImageCenterGC/LC-MSrawspectraPeaklistsSpectralbinsConcentrationtableSpectraprocessingPeakprocessingNoisefilteringMissingvalueestimationRow-wisenormalizationColumn-wisenormalizationCombinedapproachDatainputDataprocessingDatanormalizationDataintegritycheckFunctionalInterpretationStatisticalExplorationUnivariateanalysisCorrelationanalysisChemometricanalysisFeatureselectionClusteranalysisClassificationDataoverviewTwo-wayANOVAANOVA-SCATime-courseanalysisPathwayanalysisEnrichmentanalysisTopologyanalysisInteractivevisualizationOverrepresentationanalysisSinglesampleprofilingQuantitativeenrichmentanalysisOutputsResolution:
150/300/600dpiFormat:
png,tiff,pdf,svg,psProcesseddataResulttablesAnalysisreportImagesMethodscomparisionTemporaldriftBatcheffectBiolgoicalcheckingPeaksearchingPathwaymappingName/IDconversionLipidomicsMetaboAnalystOverviewRawdataprocessingDatareduction&statisticalanalysisFunctionalenrichmentanalysisMetabolicpathwayanalysisQualitycontrolanalysisDataprocessingoverviewSupporteddataformatsConcentrationtablesPeaklistsSpectralbinsRawspectra(*notrecommended)ExampleDatasetsDataProcessing6/25/2012Metabolomics20129Purpose:
toconvertvariousrawdataformsintodatamatricessuitableforstatisticalanalysisDataUploadAlternativelyDataIntegrityCheckDataNormalizationNormalizationResultQualityControlDealingwithoutliersDetectedmainlybyvisualinspectionMaybecorrectedbynormalizationMaybeexcludedDealingwithmissingvaluesNoisereductionVisualInspectionWhatdoesanoutlierlooklike?
FindingoutliersviaPCAFindingoutliersviaHeatmap6/25/2012Metabolomics201217QualityCheckModuleOutlierRemovalDataFilteringCharacteristicsofnoise&uninformativefeaturesLowintensitiesLowvariances(default)NoiseReductionMissingvalues6/25/2012Metabolomics201222DimensionReduction&StatisticalAnalysisCommontasksToidentifyimportantfeatures;Todetectinterestingpatterns;ToassessdifferencebetweenthephenotypesTofacilitateclassification/predictionANOVAViewIndividualCompoundsOverallcorrelationpatternSpecifyformatSpecifyresolutionSpecifysizeHighresolutionimageTemplateMatchingLookingforcompoundsshowinginterestingpatternsofchangeEssentiallyamethodtolookforlineartrendsorperiodictrendsinthedataBestfordatathathas3ormoregroupsTemplateMatching(cont.)Stronglinear+correlationtograin%Stronglinear-correlationtograin%PCAScoresPlotPCALoadingPlotCompoundsmostresponsibleforseparationPLS-DAScorePlotEvaluationofPLS-DAModelPLS-DAModelevaluatedbycrossvalidationofQ2andR2Morecomponentstomodelimprovesqualityoffit,buttrytominimizethisvalue3ComponentmodelseemstobeagoodcompromisehereGoodR2/Q2(0.7)ImportantCompoundsModelValidationHeatmapVisualizationHeatmapVisualization(cont.)DownloadResultsAnalysisReportMetaboliteSetEnrichmentAnalysis(MSEA)EnrichmentAnalysisPurpose:
TotestiftherearesomebiologicallymeaningfulgroupsofmetabolitesthataresignificantlyenrichedinyourdataBiologicalmeaningfulgroupsPathwaysDiseaseLocalizationCurrently,onlysupportshumanmetabolomicdataMSEAAccepts3kindsofinputfiles1)listofmetabolitenamesonly(ORA)2)listofmetabolitenames+concentrationdatafromasinglesample(SSP)3)aconcentrationtablewithalistofmetabolitenames+concentrationsformultiplesamples/patients(QEA)TheMSEAapproach45AssessmetabolitesetdirectlyCompoundconcentrationsCompoundselection(t-tests,clustering)AbnormalcompoundsCompoundconcentrationsMetabolitesetlibrariesOverRepresentationAnalysisQuantitativeEnrichmentAnalysisBiologicalinterpretationFindenrichedbiologicalthemesCompoundconcentrationsImportantcompoundlistsSingleSampleProfilingComparetonormalreferencesORAinputForMSEAStartwithacompoundListUploadCompoundListCompoundNameStandardizationNameStandardization(cont.)SelectaMetaboliteSetLibraryResultResult(cont.)TheMatchedMetaboliteSetSingleSampleProfilingSingleSampleProfiling(cont.)ConcentrationComparisonConcentrationComparison(cont.)QuantitativeEnrichmentAnalysisResultTheMatchedMetaboliteSetMetabolicPathwayAnalysisPathwayAnalysisPurpose:
toextendandenhancemetabolitesetenrichmentanalysisforpathwaysbyConsideringthestructuresofpathwayDynamicpathwayvisualizationCurrentlysupports1500pathwayscovering17organisms(basedonKEGG)NetworkTopologyJunkeretal.BMCBioinformatics200663Whichpositionsareimportant?
HubsNodesthatarehighlyconnected(redo
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