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QLUCOREOMICSEXPLORER3.3FEATUREOVERVIEW
COPYRIGHT2017QLUCOREAB
QlucoreOmicsExplorer3.3featureoverviewINTRODUCTION
QlucoreOmicsExplorer(QOE)isdevelopedtosupporttheuserwithfast,simpleandvisualanalysisofmeasureddataconsideringpubliclyavailableinformationsuchasgeneontologies,pathwaysandothersystembiologyinformationtomaximizetheoutputoftheanalysis.Youreachallkeyfunctionalitywithoneortwomouseclicksandtheresultsofyouractionsarealwayspresentedtoyouinrealtimebyavisualupdate.Thevisualapproachmakesiteasytopublishresultsaswellasworkinginteams.QlucoreOmicsExplorershipsinabasemodulewithanoptiontoaddaNGSmodulewithextensivefunctionalityforNGSdataanalysis.DetailedinformationabouttheNGSmodulefeaturesispresentedintheNGSModulefeatureoverviewdocument.QlucoreOmicsExploreristailoredforcreativeanalysiswithafocusoninstantresultsandeffectivevisualizations.
o QOEworksinfullrealtimewithboth2Dand3Dpresentationsofalldata.Allplotsaretrulyinteractive.Theuserisencouragedtoexplorethedatabychangingfiltersandparametersdynamically.
o QOEuniquelycombinespowerfulstatisticalanalysiswithinstantvisualization.Mostactionsarecontrolledwithonlyonemouseclick.
o QOEprovidessimpleworkflowsformRNA,miRNAdataandDNAMethylateddatawithdirectimportandnormalizationofAgilent,AffymetrixdataandalignedBAMfilesforRNA-seqdata.TheNGSmodulesupportsawiderangeofoptionsforNGSdata.
o TheintegratedGeneSetEnrichmentAnalysis(GSEA)workbenchallowsastraightforwardanalysisofthebiologicalcontext(pathways,ontologycategoriesoranyotherrelevantsetofgenes).
o Classifierscanbeconstructedusinganyofthefollowingmethods:SupportVectorMachines,RandomForestandkNN.
o QOEincludesanopeninterfacetoR.
o QOEsupporthierarchicalclustering,K-meansclustering,heatmapswithdendogramsandDynamicPrincipalComponentAnalysis(PCA).
o AdirectlinktoGeneExpressionOmnibus(GEO)enablesonebuttondatadownloadsandeasycomparisonoffindingswithpublishedmaterialandwiththeGOBrowseryoucanquicklysearchinontologies.
o QOEonlyrequiresanormalcomputertohandlehugedatasets(morethan100millionentries).
QLUCOREOMICSEXPLORER3.3FEATUREOVERVIEW
COPYRIGHT2017QLUCOREAB
MAINFUNCTIONALITY
o Analyzeandexploredatasetbyacombinationofvisualizationsandintuitivefilters.
o Dostatisticalanalysisusingawiderangeofbuiltintests,suchasANOVA,aswellasthroughtheopeninterfacetoR.Generateresultswithfalsediscoveryrates(q-value),foldchangeandp-values.
o Performhierarchicalclusteringandgeneratedynamicheatmapplots.
o AnalyzeRNA-seqdatabothintheGenomebrowserandaPCAplotinasynchronizedview
o Finetuneandgenerateresultsusinganycombinationofscatterplots,boxplotsandlineplots.
o InstantlycreatePrincipalComponentAnalysisPCAplotsoflargedatasetsandconfirmtheinformationcontentbyusingtheQlucoreuniquefunctionalityProjectionScore.
o UseK-means++clustering
o Useanyofseveralmethods,Hierarchicalclustering,PCA,clustering,ISOMAPandorgraphsforvisualdataexploration.
o Buildclassifiersandclassifynewsamples.
o DofunctionalanalysisinthecontextofpublicavailablegenesetssuchaspathwaysandsoonusingGSEA.
o DownloaddatafromGeneExpressionOmnibus(GEO)tocompareyourownresultswithpublishedmaterial.
o Removeunwanteddependenciessuchasartifactsandoutliers.Managebatcheffects.
o BenefitfromthestreamlinedworkflowsforAffymetrixgeneexpressionmicroarrayandAgilentmiRNAandmRNAdataaswellasdirectimportofalignedBAMfileswithRNA-seqdatafordigitalgeneexpressionanalysis.
o Keeptrackofyourworkwithpowerfulgloballogandrestorefunction.
QLUCOREOMICSEXPLORER3.3FEATUREOVERVIEW
COPYRIGHT2017QLUCOREAB
OUTPUT
o Highquality2-Dand3-Dgraphics.
o 11plottypes:Heatmap,samplePCA,variablePCA,barplot,samplescatterplot,variablescatterplot,boxplot,lineplot,histogram,Kaplan-MeierandROCcurves.
o Datatableview.
o GSEAresults;enrichmentplotsaswellasleadingedgeheatmapsandresultlists.
o Flexibleorderinginheatmap.Orderaccordingtohierarchicalclusteringoranannotationorastatisticalvalue.
o Presentmultipleannotationsinaheatmap.
o Plotbothsamplesandvariables.
o Openmultipledatasetsatonetime.
o Synchronizedplots(asmanyasyoulike).Synchronizedplotsareupdatedsimultaneously
o Variablelistswithp-values,foldchangeandFDR(q-values)valuesincludingacompletedescriptionofhowthelistwasgenerated.
o Plotarbitraryprincipalcomponents.
o Colorthesamplesandthevariablesthroughdifferentmethods.
o Colorthevariablesaccordingtoanylist.
o Labelthesamplesandthevariablesthroughdifferentmethods.
o Presentmultiplescatterplotsinoneview.
o Colorlegendwindow.Explainsthecolorsandscalesintheactiveplot.Canbeexportedwithaplot.
o Classifiers
QLUCOREOMICSEXPLORER3.3FEATUREOVERVIEW
COPYRIGHT2017QLUCOREAB
GSEAWORKBENCH
o Starttheanalysiswithonekeypress.Allplotsandlistsdirectlyavailable.
o Workwithpubliclyavailablegenesetsorworkwithyourownsets.
o Filterresultsonq-valuewithslider.
o Selectrankingcriteriafromabroadrange(SNR,twogroupcomparison,multigroup).
o ExportselectedlistsasvariableliststobeusedinOEmainwindow.
o Exportplotsandlistsforpublicationandfurtheranalysis
GOBROWSER
o Useanyontologythatyouprefer.
o Excellentoverviewbybothtreeandflatviewofresults.
o Veryfastsearch.
o ExportlistsasvariableliststobeusedinOEmainwindow.
EDITINGOFDATA
o Interactiveeditingofsampleannotations.
o Interactiveeditingofvariablelists.
o Variablecollapse.Selectanyvariableannotationandcollapse1thedataonthisannotation.
1Combineinformationfromoneortwovariablestoanewvariable.Example:twomeasauredvariabelsmatchoneGeneandthestudyshouldbeconductedongenelevel.
QLUCOREOMICSEXPLORER3.3FEATUREOVERVIEW
COPYRIGHT2017QLUCOREAB
SELECTIONS
o Workwithsubsetsofsamplesandvariables.
o Selectsamplesbasedonclinicalvariablesandotherannotations.
o Selectvariablesbasedonvariance,F-test(ANOVA),t-test,rankcorrelation,correlationcoefficients,Foldchange,annotationsearchesandimportedvariablelists(suchaspathways).
o Selectvariablesbasedonstatisticalmethodsfromtheopeninterface.Seebelow.
o Selectvariablesbasedonlinearorquadraticregression
o Studypartofdatasetbasedonimportedvariablelists(suchaspathways)andorcombinationsoflists.
VARIABLELISTS
o Automaticvariablelistforallactivevariables.
o AutomaticvariablelistforSearchresults.
o Setoperationsonvariablelists.
o Coloranyvariableplotaccordingtoanyselectionofvariablelists.
o Savevariablelistsincludinginformationabouthowtheywascreated,thishelpsincreatinggoodresulttraceability
VERIFICATION
o ProjectionscoretounderstandhowmuchinformationthatiscapturedinaPCAplot.
o Getdirectfeedbackonp-valuesandq-valuesduringvariableselection.
o Verifyresultsbyredoingtheanalysiswithpermutedsampleannotationsorwithrandomnumbers.
o Verifyresultsthroughremove-one-at-a-timecrossvalidationorseveralatthetimecrossvalidation.
o ContinuousupdateoncapturedvarianceinPCAplot.
QLUCOREOMICSEXPLORER3.3FEATUREOVERVIEW
COPYRIGHT2017QLUCOREAB
o Generatehistogramstocheckvariabledistributions.
o Generateboxplotstovisualizeresults.
CLUSTERSANDNETWORKS
o Visualizesampleclustersbyconnectingeachsamplewithitsnearestneighbors.
o Visualizevariableclustersbyconnectingcorrelatedvariables.
o CreateclustersusingK-means++.
o Performhierarchicalclusteringintheheatmapplot
CLASSIFICATION
o BuildclassifierswithSupportVectorMachines,RandomTreesorkNN.
o Validatetheclassifiereitherontheinternaldatasetwithcrossvalidationschemeoranexternaldataset.
o Classifynewsamplesbasedonthebuildclassifier.
BATCHCORRECTIONS
o Correctmultiplebatcheffectsusingin-builtmethods.
OPENINTERFACE
o InterfacetoR
o Expandstheavailablestatisticaltests.
QLUCOREOMICSEXPLORER3.3FEATUREOVERVIEW
COPYRIGHT2017QLUCOREAB
o Worksfortwo-group,pairedtestsandmultigroups,withorwithouteliminatedfactors.
o Exampleonsupportedmethodsare:Limma,Wilcoxon,Welch,…
IMPORT
o Affymetrix.celfilesand.chpfiles.IncludingnormalizationandgenerationofQC-report.
o AgilentTextFiles(*.txt)(fromFeatureExtractionSoftware).OEimportsandnormalizesmiRNAdata,mRNAdataandDNAmethylateddata.Bothsinglecolorandtwocolorarrayscanbehandled.
o AgilentGeneViewfiles(*.txt)formiRNAdata.
o AlignedBAMfileswithRNA-seqdata.
o Flexibleimportwizardforimportof(*.txt,*.csv,*.tsv)files.
o Datafilesof.gedataformat(normalortransposed).
o Annotationfiles,bothsamplesandvariables(*.txt,*.csv).
o Basicfileformatssuchaso Datafilesof.txtformat(onevariableidentifiercolumnandonesampleidentifierrow).CalledSimple
textfiles.o CompactTextfiles(*.csv)
o Data(GDSandGSE)fromGeneExpressionOmnibus(GEO).Directdownload.
o GEOsoftfiles(*.softand*.soft.gz).
o GEOSeriesMatrix(*.txtand*.txt.gz).
o GenesetfilesfortheGSEAWorkbench(*.txtand*.gmt).
o Ontologyfiles(*.obo,*.obo.xml,obo-xeml.gz,obo-xml).
o Variablelists
o DirectNetAffximport
o AffymetrixCHPandARRfiles
o Logfiles
QLUCOREOMICSEXPLORER3.3FEATUREOVERVIEW
COPYRIGHT2017QLUCOREAB
o Qualitycontrolplotfiles
o Createdclassifiers
o Datafilesof.cedataformat
EXPORT
o Stillimages(plots)includingalegendplot.Selectresolutionandtheplotisexported.
o Datafiles
o Variablelists(withannotationsanddataifsopreferred)
o Videos
o Logfiles
o Correlationandco-variancematrixes
o QC-report
o PCAloadings
o PCAplotcoordinates
o Classifiers
OTHER
o Missingvaluereconstruction(twoversions)
o Variablenormalization
o Multi-dimensionalrescaling
o Isomap
o Takelogarithmofdata
o SimplifiedAffymetrixannotations
QLUCOREOMICSEXPLORER3.3FEATUREOVERVIEW
COPYRIGHT2017QLUCOREAB
RESEARCHPURPOSEONLY
QlucoreOmicsExplorerisonlyintendedforresearchpurposes.
DISCLAIMER
Thecontentsofthisdocumentaresubjecttorevisionwithoutnoticeduetocontinuousprogressinmethodology,design,andmanufacturing.
Qlucoreshallhavenoliabilityforanyerrorordamagesofanykindresultingfromtheuseofthisdocument.
TRADEMARKLIST
NetAffxisatrademarkofAffymetrix
CREDITS
GSEA:Subramanian,Tamayo,etal.2005ProcNatlAcadSciUSA102(43):15545-50
TheGeneOntologyConsortium."Geneontology:toolfortheunificationofbiology."Nat.Genet..May2000;25(1):25-9.
RCoreTeam(2014).R:Alanguageandenvironmentforstatisticalcomputing.RFoundationforStatisticalComputing,Vienna,Austria,http://www.R-project.org/.
