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DAVIDDatabaseforAnnotation,VisualizationandIntegratedDiscoveryDAVID

providesacomprehensivesetoffunctionalannotationtoolsforinvestigatorstounderstandbiologicalmeaningbehindlargelistofgenes

Identifyenrichedbiologicalthemes,particularlyGOterms

Discoverenrichedfunctional-relatedgenegroups

Clusterredundantannotationterms

VisualizegenesonBioCarta&KEGGpathwaymaps

Displayrelatedmany-genes-to-many-termson2-Dview.

Searchforotherfunctionallyrelatedgenesnotinthelist

ListinteractingproteinsExploregenenamesinbatchLinkgene-diseaseassociationsHighlightproteinfunctionaldomainsandmotifs

Redirecttorelatedliteratures

Convertgeneidentifiersfromonetypetoanother.GeneListManagerDAVIDAnalyticModulesAnygivengeneisassociatingwithasetofannotationterms.Ifgenessharesimilarsetofthoseterms,theyaremostlikelyinvolvedinsimilarbiologicalmechanisms.Thealgorithmadoptskappastatisticstoquantitativelymeasurethedegreeoftheagreementhowgenessharethesimilarannotationterms.Kapparesultrangesfrom0to1.ThehigherthevalueofKappa,thestrongertheagreement.Kappamorethan0.7typicallyindicatesthatagreementoftwogenesarestrong.Kappavaluesgreaterthan0.9areconsideredexcellent.

ParameterPanelGeneClustersIdentifiedbyDAVIDUser’sgeneIDs&Names12Viewandselectannotationcategoriesofyourinterests333Percentage,e.g.44/163GenesfromthelistinvolvedinthisannotationcategorySinglechartreportonlyforthisAnnotationcategories

TablereportforallSelectedannotationcategoriesLinearorredundantchartreportofannotationtermsforallselectedannotationcategoriesaboveClusteredornon-redundantchartreportofannotationtermsforallselectedannotationcategoriesaboveDAVIDGeneIDConversionTool(DGCT)Ifasignificantportion(>20%)ofinputgeneIDsfailtobemappedtoaninternalDAVIDID,aspeciallydesignedmodule,theDAVIDGeneIDConversionTool,willstartuptohelpmapsuchIDs.DAVIDGeneNameBatchViewerThegenenamebatchviewerisabletoquicklyattachmeaningtoalistofgeneIDsbyrapidlytranslatingthemintotheircorrespondinggenenames.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,givessharpersepa

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