GSEA分析

GeneSetEnrichmentAnalysis1.Introduction.2.GSEASoftware3.DataFormats4.UsingGSEA5.GSEAOutput6.GSEAResultsGeneSetEnrichmentAnalysis-GSEA-MITBroadInstitutev2.0availablesinceJan2007v2.0.1availablesinceFeb16th2007Version2.0includesBiocarta,BroadInstitute,GeneMAPP,KEGGannotationsandmore...Platforms:Affymetrix,Agilent,CodeLink,custom...GSEA(Subramanianetal.PNAS.2005.)GeneSetEnrichmentAnalysis-GSEA-:::HowworksGSEA?DatasetdistributionNumberofgenesGeneExpressionLevelGeneSetEnrichmentAnalysis-GSEA-:::K-StestGeneset1distributionGeneset2distributionClassAClassBttestcut-offFDR0.05FDR0.05...testinggenesindependently...Biologicalmeaning?GeneSetEnrichmentAnalysis-GSEA-:::HowworksGSEA?ES/NESstatistic-+ClassAClassBGeneSet1ttestcut-offGeneSet2GeneSet3Geneset3enrichedinClassBGeneset2enrichedinClassAGeneSetEnrichmentAnalysis-GSEA-:::Introduction.:::HowworksGSEA?GeneSetEnrichmentAnalysis-GSEA-:::Introduction.ESexamples:::NESpvalFDRGeneSetEnrichmentAnalysis-GSEA-:::Introduction.TheEnrichmentScore:::Benjamini-Hochberg:::Contents.1.Introduction.2.GSEASoftware3.DataFormats4.UsingGSEA5.GSEAOutput6.GSEAResultsGeneSetEnrichmentAnalysis-GSEA-:::GSEAsoftware.Download:::GeneSetEnrichmentAnalysis-GSEA-:::GSEAsoftware.MainWindow:::GeneSetEnrichmentAnalysis-GSEA-Loadingdata:::!!!GeneSetEnrichmentAnalysis-GSEA-:::GSEAsoftware.RunningGSEA:::GeneSetEnrichmentAnalysis-GSEA-:::GSEAsoftware.LeadingEdgeAnalysis:::GeneSetEnrichmentAnalysis-GSEA-:::GSEAsoftware.ChiptoChipMapping:::MSigDB::::::Contents.1.Introduction.2.GSEASoftware3.DataFormats4.UsingGSEA5.GSEAOutput6.GSEAResultsGeneSetEnrichmentAnalysis-GSEA-:::DataFormats.GeneSetEnrichmentAnalysis-GSEA-:::DataFormats.GeneSetEnrichmentAnalysis-GSEA-Expressiondatasets::::::DataFormats.*.gctGeneSetEnrichmentAnalysis-GSEA-Expressiondatasets::::::DataFormats.*.resGeneSetEnrichmentAnalysis-GSEA-Expressiondatasets::::::DataFormats.*.pclGeneSetEnrichmentAnalysis-GSEA-Expressiondatasets::::::DataFormats.*.txt*.clsGeneSetEnrichmentAnalysis-GSEA-Phenotypedatasets::::::DataFormats.Forcategoricalphenotypes(e.g.TumorvsControl)GeneSetEnrichmentAnalysis-GSEA-Phenotypedatasets::::::DataFormats.Forcontinuousphenotypes(e.g.GenecorrelatedtoGeneSet)Forcontinuousphenotypes(e.g.GenevsTimeSeries)Timeserie(each30minutes)PeakprofilewantedGeneSetEnrichmentAnalysis-GSEA-GeneSetDatabase::::::DataFormats.*.gmxGeneSetEnrichmentAnalysis-GSEA-GeneSetDatabase::::::DataFormats.*.gmtGeneSetEnrichmentAnalysis-GSEA-Rankedlistformat::::::DataFormats.*.rnk:::Contents.1.Introduction.2.GSEASoftware3.DataFormats4.UsingGSEA5.GSEAOutput6.GSEAResultsGeneSetEnrichmentAnalysis-GSEA-:::UsingGSEA.Loadingdata:::GeneSetEnrichmentAnalysis-GSEA-:::UsingGSEA.Loadingdata:::GeneSetEnrichmentAnalysis-GSEA-RunningGSEA::::::UsingGSEA.GeneSetEnrichmentAnalysis-GSEA-:::MSigDB.gsea_home:::UsingGSEA.GeneSetEnrichmentAnalysis-GSEA-RunningGSEA::::::UsingGSEA.1.Choosetrue(default)tohaveGSEAcollapseeachprobesetinyourexpressiondatasetintoasinglegenevector,whichisidentifiedbyitsHUGOgenesymbol.Inthiscase,youareusingHUGOgenesymbolsfortheanalysis.ThegenesetsthatyouusefortheanalysismustuseHUGOgenesymbolstoidentifythegenesinthegenesets.2.Choosefalsetouseyourexpressiondatasetasis.Inthiscase,youareusingtheprobeidentifiersthatareinyourexpressiondatasetfortheanalysis.Thegenesetsthatyouusefortheanalysismustalsousetheseprobeidentifierstoidentifythegenesinthegenesets.GeneSetEnrichmentAnalysis-GSEA-RunningGSEA:::PhenotypeGeneSets(fewsamples):::UsingGSEA.GeneSetEnrichmentAnalysis-GSEA-RunningGSEA::::::UsingGSEA.GeneSetEnrichmentAnalysis-GSEA-Chip2Chipmapping:::Chip2ChiptranslatesthegeneidentifiersinagenesetsfromHUGOgenesymbolstotheprobeidentifiersforaselectedDNAchip.:::UsingGSEA.GeneSetEnrichmentAnalysis-GSEA-Enrichmentstatistic:::Tocalculatetheenrichmentscore,GSEAfirstwalksdowntherankedlistofgenesincreasingarunning-sumstatisticwhenageneisinthegenesetanddecreasingitwhenitisnot.Theenrichmentscoreisthemaximumdeviationfromzeroencounteredduringthatwalk.Thisparameteraffectstherunning-sumstatisticusedfortheanalysis.:::UsingGSEA.GeneSetEnrichmentAnalysis-GSEA-RankingMetric:::Signal2NoisetTestCosineEuclideanManhattenPearson(timeseries)RatioofClassesDiffofClassesLog2_Ratio_of_ClassesCategoricalphenotypesContinuousphenotypes:::UsingGSEA.GeneSetEnrichmentAnalysis-GSEA-RankingMetric::::::UsingGSEA.GeneSetEnrichmentAnalysis-GSEA-RankingMetric::::::UsingGSEA.GeneSetEnrichmentAnalysis-GSEA-real8.28.18.0…-7.5-7.7-7.9abs8.28.18.07.97.77.5…parametertodeterminewhethertosortthegenesindescending(default)orascendingorder.Moreparameters::::::UsingGSEA.GeneSetEnrichmentAnalysis-GSEA-LaunchingAnalysis::::::UsingGSEA.:::Contents.1.Introduction.2.GSEASoftware3.DataFormats4.UsingGSEA5.GSEAOutput6.GSEAResultsGeneSetEnrichmentAnalysis-GSEA-:::GSEAoutput.ResultsAccession:::/Users/yourhome/gsea_homeC:\Documentsandsettings\username\gsea_homeBydefaultingsea_home:::Contents.1.Introduction.2.GSEASoftware3.DataFormats4.UsingGSEA5.GSEAOutput6.GSEAResultsGeneSetEnrichmentAnalysis-GSEA-:::GS