蛋白质Geneontology,KEGG分析软件David使用方法介绍

DAVIDDatabaseforAnnotation,VisualizationandIntegratedDiscoveryDAVIDprovidesacomprehensivesetoffunctionalannotationtoolsforinvestigatorstounderstandbiologicalmeaningbehindlargelistofgenesIdentifyenrichedbiologicalthemes,particularlyGOtermsDiscoverenrichedfunctional-relatedgenegroupsClusterredundantannotationtermsVisualizegenesonBioCarta&KEGGpathwaymapsDisplayrelatedmany-genes-to-many-termson2-Dview.SearchforotherfunctionallyrelatedgenesnotinthelistListinteractingproteinsExploregenenamesinbatchLinkgene-diseaseassociationsHighlightproteinfunctionaldomainsandmotifsRedirecttorelatedliteraturesConvertgeneidentifiersfromonetypetoanother.GeneListManagerDAVIDAnalyticModulesAnygivengeneisassociatingwithasetofannotationterms.Ifgenessharesimilarsetofthoseterms,theyaremostlikelyinvolvedinsimilarbiologicalmechanisms.Thealgorithmadoptskappastatisticstoquantitativelymeasurethedegreeoftheagreementhowgenessharethesimilarannotationterms.Kapparesultrangesfrom0to1.ThehigherthevalueofKappa,thestrongertheagreement.Kappamorethan0.7typicallyindicatesthatagreementoftwogenesarestrong.Kappavaluesgreaterthan0.9areconsideredexcellent.ParameterPanelGeneClustersIdentifiedbyDAVIDUser’sgeneIDs&Names12Viewandselectannotationcategoriesofyourinterests333Percentage,e.g.44/163GenesfromthelistinvolvedinthisannotationcategorySinglechartreportonlyforthisAnnotationcategoriesTablereportforallSelectedannotationcategoriesLinearorredundantchartreportofannotationtermsforallselectedannotationcategoriesaboveClusteredornon-redundantchartreportofannotationtermsforallselectedannotationcategoriesaboveDAVIDGeneIDConversionTool(DGCT)Ifasignificantportion(20%)ofinputgeneIDsfailtobemappedtoaninternalDAVIDID,aspeciallydesignedmodule,theDAVIDGeneIDConversionTool,willstartuptohelpmapsuchIDs.DAVIDGeneNameBatchViewer1.ThegenenamebatchviewerisabletoquicklyattachmeaningtoalistofgeneIDsbyrapidlytranslatingthemintotheircorrespondinggenenames.2.beforeproceedingtoanalysiswithothermorecomprehensiveanalytictools,investigatorscanquicklyglanceatthegenenamestofurthergaininsightabouttheirstudyandtoanswerquestions.DAVIDGeneFunctionalclassificationTheFunctionalClassificationToolgeneratesagene-to-genesimilaritymatrixbasedsharedfunctionalannotationusingover75,000termsfrom14functionalannotationsources.Thenovelclusteringalgorithmsclassifieshighlyrelatedgenesintofunctionallyrelatedgroups.SimilarityTermOverlap(anyvalue=0;default=4):theminimumnumberofannotationtermsoverlappedbetweentwogenesinordertobequalifiedforkappacalculation.SimilarityThreshold(anyvaluebetween0to1;Default=0.35):theminimumkappavaluetobeconsideredbiologicalsignificant.InitialGroupMembers(anyvalue=2;default=4):theminimumgenenumberinaseedinggroup,whichaffectstheminimumsizeofeachfunctionalgroupinthefinal.FinalGroupMembers(anyvalue=2;default=4):theminimumgenenumberinonefinalgroupafter“cleanup”procedure.Multi-linkageThreshold(anyvaluebetween0%to100%;default=50%):Itcontrolshowseedinggroupsmergeeachother,i.e.twogroupssharingthesamegenemembersoverthepercentagewillbecomeonegroup.Thehigherpercentage,ingeneral,givessharperseparationi.e.itgeneratesmorefinalfunctionalgroupswithmoretightlyassociatedgenesineachgroup.Inaddition,changingtheparameterdoesnotcontributeextragenesintounclusteredgroup.