Software options for the analysis of micorarray data
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1 Softwareoptionsfortheanalysisofmicorarraydatapage 1 Softwareoptions fortheanalysisofmicorarraydata TableofContents 1 Generalintroductiononmicroarrays: Commercialmicroarraytypes: SuggestedreadingonStatisticalmethods: Statisticalmethodscomparisons Microarrayanalysistechniques Affymetrixreading GeneExpressionAnalysis DifferentialAnalysis/MarkerSelection ClassPrediction(SupervisedLearning) ClassDiscovery(UnsupervisedLearning) PathwayAnalysis Imagingsoftware Analysissoftware Commercial Publicoropensource AffymetrixTools(free;freeregistrationrequired): MicroarraySoftwareSuite ( PubliclyAvailableSoftwareTools AdditionalTools GeneOntologiesandPathways ToolsforGeneOntologiesandPathways Genelistsmanipulations GeneLists VennDiagrams DataRepositoriesformicroarraydata...11
2 Softwareoptionsfortheanalysisofmicorarraydatapage 2 1 General introduction on microarrays: WIKI.DNAmicroarray: NIH:An(Opinionated)GuidetoMicroarrayDataAnalysis Experimentaldesign/Pooling: FreePDFbook(Finland):"DNAMicroarrayDataAnalysis,secondedition /arraybook_overview 2 Commercial microarray types: Brand Link Processedat GEC* Affymetrix Yes Roche Yes Nimblegen Spotted Arrays Yes** Brand Link ProcessedatGEC* Agilent No Combimatrix No Illumina No AppliedMicroarrays No *GEC:GeneExpressionCenter,UniversityofWisconsin Madison **Inhousemethods 3 Suggested reading on Statistical methods: 3.1 Statisticalmethodscomparisons IanBJeffery,DesmondGHiggins,AedínCCulhane(2006),"Comparisonand evaluationofmethodsforgeneratingdifferentiallyexpressedgenelistsfrom microarraydata",bmcbioinformatics,7: /7/359
3 Softwareoptionsfortheanalysisofmicorarraydatapage 3 Abstractexcerpt: Firstlywefoundlittleagreementingenelistsproducedbythe differentmethods.only8to21%ofgeneswereincommonacrossall10feature selectionmethods.secondly,weevaluatedtheclasspredictionefficiencyofeachgene listintrainingandtestcross validationusingfoursupervisedclassifiers. 3.2 Microarrayanalysistechniques Affymetrixreading GeneChip ExpressionAnalysis DataAnalysisFundamentals Chapter1OverviewofExperimentalDesignStrategy Chapter2TypesofExperimentalDesigns Chapter3DataFlowandInformaticsTools Chapter4First OrderDataAnalysisandDataQualityAssessment Chapter5StatisticalAlgorithmsReference Chapter6StatisticalAnalysis Chapter7BiologicalInterpretationofGeneChip ExpressionData Chapter8AnnotationMiningTools SamplePoolingforMicroarrayAnalysis:AStatisticalAssessmentofRisksandBiases 4 Gene Expression Analysis Therearefourbroadcategoriesofgeneexpressionanalysis: 4.1 DifferentialAnalysis/MarkerSelection Differentialanalysis,alsoknownasmarkerselection,isthesearchforgenesthatare differentiallyexpressedindistinctphenotypesusingeithere.g.thesignal to noise ratioorthet teststatistic. 4.2 ClassPrediction(SupervisedLearning) Supervisedlearning,alsoknownasclassprediction,isthesearchforagene expressionsignaturethatpredictsclass(phenotype)membership.thebasic methodologyforclasspredictionistostartwithtwodatasets,atrainingsetandtest set;useyourtrainingdatasettobuildaclassifier(classpredictor)basedonyour chosenclassificationmethod;anduseyourtestdatasettotesttheclassifier.
4 Softwareoptionsfortheanalysisofmicorarraydatapage ClassDiscovery(UnsupervisedLearning) Unsupervisedlearning,alsoknownasclassdiscovery,isthesearchforabiologically relevantunknowntaxonomyidentifiedbyageneexpressionsignatureora biologicallyrelevantsetofco expressedgenes. Thebasicmethodologyforclassdiscoveryisclustering:thedataisclusteredbased onachosenclusteringmethodandthentheclustersisvalidatedthroughgene annotations,enrichmentanalysis(aretheclustersenrichedbygenesfrom functionallyimportantcategories,pathways,orprocesses),orbyreplicatingthe resultsinotherdatasets. 4.4 PathwayAnalysis Pathwayanalysisisthesearchforsetsofgenesdifferentiallyexpressedindistinct phenotypes.genesetenrichmentanalysis(gsea)determineswhetheranapriori definedsetofgenesshowsstatisticallysignificant,concordantdifferencesbetween twobiologicalstates(e.g.phenotypes). 5 Imaging software Mostareproprietary,forreferenceonly. Name Imagene GenePixPro Nimblescan Spotfinder Notes Pro.html Analysis software 6.1 Commercial Name Notes(inuseatGEC) ArrayStar products arraystar.aspx ArrayStarv2.1:usefulforgeneexpressionruns.Readsdatafiles fromaffymetrix,illuminaandrochenimblegen.imports.txt filesforspottedarrayrunsanddatafromothersources. 2 Partek Genomics SuiteTM weeksfreetrial Partek GenomicsSuiteTM(PartekGS)isacomprehensive suiteofadvancedstatisticsandinteractivedatavisualization specificallydesignedtoreliablyextractbiologicalsignalsfrom noisydata. 2weeksFreetrial
5 Softwareoptionsfortheanalysisofmicorarraydatapage 5 Name GenSpringGX (Agilent) GenePixPro GCOS(GeneChip OperatingSoftware Affymetrix) GeneChip CommandConsole Software(AGCC) GeneSifter (Geospiza) MatLab (MathWorks) SpotFire (TIBCO) Notes 2weeksfreetrialdownload support.com/user/register ix Pro.html ific/gcos.affx (REPLACEDBYAGCC,SEEBELOW) (ReplacesGCOS) Web basedexpressionanalysissoftwarewithstatisticaland visualtools.(freetrial) CaseStudy:SpotfireDrivesMicroarrayAnalysisatthe UniversityofWashington: Studies/University Washington.ashx 6.2 Publicoropensource Affymetrix Tools (free; free registration required): ExpressionConsole NetAffx SoftwarefreelyprovidedbyAfftymetrixforextractingdata from.celand.datfileswithvariousbackgroundcorrection, normalizationandsummarizationmethods. ific/expression_console_software.affx EnablesresearcherstocorrelatetheirAffymetrixGeneChip arrayresultswitharraydesignandannotationinformation Microarray Software Suite ( ) MADAM: MicroArrayDAta Manager Spotfinder TheMicroarrayDataManager,implementedinJava,facilitates theentryofdataintoarelationaldatabase. TIGRSpotfinderreadspaired16 bitor8 bittiffimagefiles
6 Softwareoptionsfortheanalysisofmicorarraydatapage 6 MIDAS:Microarray DataAnalysis System MeV: MultiExperiment Viewer AMP:Automated MicroarrayPipeline generatedbymostmicroarrayscannersforthethe quantificationofgeneexpression. MIDASisanormalizationtooltohelpcompensatefor variabilitybetweenslidesandfluorescentdyes,aswellas othersystematicsourcesoferror.datafiltering:removepoor orquestionabledata.. Normalizedandfilteredexpressionfilescanbeanalyzedusing TIGRMultiexperimentViewer(MeV).MeVisaversatile microarraydataanalysistool,incorporatingsophisticated algorithmsforclustering,visualization,classification, statisticalanalysisandbiologicalthemediscovery.mevcan handleseveralinputfileformats.theseincludethe.mev and.tav filesgeneratedbytigrspotfinderandtigrmidas,and alsoaffymetrix (.txt )andgenepix (.gpr )files. WehaveassembledaguidefornormalizingAffymetrix.CEL files,whichcoversrmaexpress,bioconductor,andamp. Web-based application that allows the normalization of microarray data. AMP Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options on the following pages. AMP will performs data normalization (e.g. RMA), basic statistical analysis (e.g. t-test, ANOVA), and analysis of annotation using gene classification (e.g. Gene Ontology term assignment). The analyses are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis Publicly Available Software Tools Bioconductor Source: SAM dchip stat.stanford.edu/~tibs/sam/ SAMreportslocalfalsediscoveryratesandmissrates.Italso handlestimecoursedata,doesnon parametrictestsandpattern discovery. Anopensourceandopendevelopmentsoftwareprojectforthe analysisandcomprehensionofgenomicdata
7 Softwareoptionsfortheanalysisofmicorarraydatapage 7 DNA ChipAnalyzer(dChip)isasoftwarepackageforprobe level andhigh levelanalysisofaffymetrixgeneexpressionmicroarrays andsnpmicroarrays.reference:liandwongpaperinpnas,jan2, 2001Vol98No RMA express Aprogramtocomputegeneexpressionsummaryvaluesfor AffymetrixGeneChip datausingtherobustmultichipaverage expressionsummary.rmaconsistsofthreesteps:abackground adjustment,quantilenormalization,andfinallysummarization. BRB ArrayTools ArrayTools.html BRBArrayToolsisanintegratedpackageforthevisualizationand statisticalanalysisofdnamicroarraygeneexpressiondata. DevelopedattheNationalCancerInstitute Additional Tools GenePattern DownloadoruseWeb basedversion. IntendedAudiences:Biomedicalresearchers.Areasoffocusinclude: MicroarrayAnalysis,SNPAnalysis,Proteomics. AreaofFocus:DataAnalysisandStatisticalTools LocalTools(MadisonCampus) EZarray Web based.workswithr/bioconductorinthebackground ServeraccessibleonlyfromCampus 7 Gene Ontologies and Pathways There are tools to look at Gene Ontology and potential pathways to which your genes of interest may belong. 7.1 ToolsforGeneOntologiesandPathways (Source: Gene Expression TheGeneExpressionOmnibusisahigh throughputgeneexpression/ Omnibus molecularabundancedatarepository,aswellasacurated,online resourceforgeneexpressiondatabrowsing,queryandretrieval. Gene Ontologies TheGeneOntologyprojectprovidesacontrolledvocabularytodescribe geneandgeneproductattributesinanyorganism.
8 Softwareoptionsfortheanalysisofmicorarraydatapage 8 Affymetrix Gene Ontology Mining Tool AffymetrixhasitgeneontologysoftwareembeddedwithinitsNetAffx onlineanalysiscenter. GOManual: ErmineJ Afreesoftwareforgeneexpressionanalysisinthecontextoffunctional categories(e.g.,geneontology).erminejperformsanalysesof"gene sets"inexpressionmicroarraydata.atypicalgoalistodetermine whetherparticularbiologicalpathwaysare"doingsomething interesting"inthedata.thesoftwareisdesignedtobeusedby biologistswithlittleornoinformaticsbackground. BRB ArrayTools ArrayTools.html ThisapproachisincludedforgenesetsbasedonGeneOntology categories,biocartapathways,keggpathwaysandforuser specified genesets.thepowerofthemethodisbasedontwofactors.first,since thenumberofgenesetsisusuallymuchlessthanthenumberof individualgenes,thepenaltyformultiplecomparisonsismuchless. Thisappliesregardlessofthemethodusedtocontrolformultiple comparisons,beitcontrollingthefalsediscoveryrateormore traditionalmethods.thesecondfactoristhatagenesetcanbe identifiedassignificantifmanyofthecomponentgenesare differentiallyexpressed,butnoneindividuallyatasufficientlystrong leveltopassthestringentthresholdnecessitatedbythemultiple comparisonpenalty.inanalysisofdataihavefoundseveralinstances whereindividualgeneanalysisresultedinveryfewdifferentially expressedgenes,butanalysisofgenesetsidentifiedhighlysignificant GOcategoriesandsignallingpathwaysthatwerebiologicallyimportant. Pathguide Websiteresourcewithinformationofabout325biologicalpathway andmolecularinteractionrelatedresources. KEGG PATHWAY Database KEGG:KyotoEncyclopediaofGenesandGenomes. KEGGPATHWAYisacollectionofmanuallydrawnpathwaymaps representingourknowledgeonthemolecularinteractionandreaction networksfor:1.metabolism2.geneticinformationprocessing 3.EnvironmentalInformationProcessing4.CellularProcesses 5.HumanDiseases6.DrugDevelopment(structurerelationships.KEGG drugstructuremaps) GenMAPP Afreecomputerapplicationdesignedtovisualizegeneexpressionand othergenomicdataonmapsrepresentingbiologicalpathwaysand groupingsofgenes.
9 Softwareoptionsfortheanalysisofmicorarraydatapage 9 Cytoscape NetworkDataIntegration,Analysis,andVisualizationinaBox Cytoscapeisanopensourcesoftwareplatformforvisualizingcomplex networksandintegratingthesewithanytypeofattributedata. 8 Gene lists manipulations. 8.1 GeneLists DAVID DatabaseforAnnotation,VisualizationandIntegratedDiscovery (DAVID) FunctionalAnnotation Gene annotationenrichmentanalysis,functionalannotation clustering,biocarta&keggpathwaymapping,gene disease association,homologuematch,idtranslation,literaturematchand more GeneFunctionalClassification Providearapidmeanstoreducelargelistsofgenesintofunctionally relatedgroupsofgenestohelpunravelthebiologicalcontent capturedbyhighthroughputtechnologies.more GeneIDConversion ConvertlistofgeneID/accessionstoothersofyourchoicewiththe mostcomprehensivegeneidmappingrepository.theambiguous accessionsinthelistcanalsobedeterminedsemi automatically. More GeneNameBatchViewer Displaygenenamesforagivengenelist;Searchfunctionallyrelated geneswithinyourlistornotinyourlist;deeplinkstoenriched detailedinformation.
10 Softwareoptionsfortheanalysisofmicorarraydatapage VennDiagrams genenvenn CreationofVenndiagramfrom2or3listsofgenes. Programgenevenn exampleofvenndiagramfor3lists venny Forupto4lists! Note:VenndiagramscanalsobecreatedwithinR.Forexamplethelimmapackage hascommandvenndiagram()forupto3lists. ThecommercialPartekGenenomicsSuitecanplotVenndiagramsforupto5lists.
11 Softwareoptionsfortheanalysisofmicorarraydatapage 11 9 Data Repositories for microarray data. Repositories NCBI'sGEO ArrayExpress Stanford Microarray Database TheGene Expression Database (GXD) Yale Microarray Database Ahigh throughputgeneexpression/molecularabundancedata repository,aswellasacurated,onlineresourceforgeneexpression databrowsing,queryandretrieval. ArrayExpressisapublicrepositoryformicroarraydata,aimedat storingwellannotateddatainaccordancewithmged recommendations.runbyeuropeanbioinformaticsinstitute (MGED: Storesrawandnormalizeddatafrommicroarrayexperiments,as wellastheircorrespondingimagefiles.inaddition,smdprovides interfacesfordataretrieval,analysisandvisualization. Acommunityresourceforgeneexpressioninformationfromthe laboratorymouse.gxdstoresandintegratesdifferenttypesof expressiondataandmakesthesedatafreelyavailableinformats appropriateforcomprehensiveanalysis. TheYaleMicroarrayDatabaseProjectisacollaborativeeffort betweenseverallaboratoriesandcenterstoarchivemicroarray imagesandprovidestatisticaltoolsthroughawebinterface. Notes
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