蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件

DAVIDDatabaseforAnnotation,VisualizationandIntegratedDiscoveryDAVIDDatabaseforAnnotation,DAVID

providesacomprehensivesetoffunctionalannotationtoolsforinvestigatorstounderstandbiologicalmeaningbehindlargelistofgenes

Identifyenrichedbiologicalthemes,particularlyGOtermsDiscoverenrichedfunctional-relatedgenegroups

ClusterredundantannotationtermsVisualizegenesonBioCarta&KEGGpathwaymapsDisplayrelatedmany-genes-to-many-termson2-Dview.SearchforotherfunctionallyrelatedgenesnotinthelistListinteractingproteinsExploregenenamesinbatchLinkgene-diseaseassociationsHighlightproteinfunctionaldomainsandmotifsRedirecttorelatedliteraturesConvertgeneidentifiersfromonetypetoanother.DAVID

providesacomprehensi蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件GeneListManagerGeneListManager蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件DAVIDAnalyticModulesDAVIDAnalyticModules蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件Anygivengeneisassociatingwithasetofannotationterms.Ifgenessharesimilarsetofthoseterms,theyaremostlikelyinvolvedinsimilarbiologicalmechanisms.Thealgorithmadoptskappastatisticstoquantitativelymeasurethedegreeoftheagreementhowgenessharethesimilarannotationterms.Kapparesultrangesfrom0to1.ThehigherthevalueofKappa,thestrongertheagreement.Kappamorethan0.7typicallyindicatesthatagreementoftwogenesarestrong.Kappavaluesgreaterthan0.9areconsideredexcellent.

Anygivengeneisassociating蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件ParameterPanelGeneClustersIdentifiedbyDAVIDUser’sgeneIDs&NamesParameterPanelGeneClustersU蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件12Viewandselectannotationcategoriesofyourinterests333Percentage,e.g.44/163GenesfromthelistinvolvedinthisannotationcategorySinglechartreportonlyforthisAnnotationcategories

12ViewandselectannotationcTablereportforallSelectedannotationcategoriesTablereportforallSelected蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件LinearorredundantchartreportofannotationtermsforallselectedannotationcategoriesaboveLinearorredundantchartrepo蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件Clusteredornon-redundantchartreportofannotationtermsforallselectedannotationcategoriesaboveClusteredornon-redundantcha蛋白質Geneontology-KEGG分析軟件David使用方法介紹課件DAVIDGeneIDConversionTool(DGCT)Ifasignificantportion(>20%)ofinputgeneIDsfailtobemappedtoaninternalDAVIDID,aspeciallydesignedmodule,theDAVIDGeneIDConversionTool,willstartuptohelpmapsuchIDs.DAVIDGeneIDConversionToolDAVIDGeneNameBatchViewerThegenenamebatchviewerisabletoquicklyattachmeaningtoalistofgeneIDsbyrapidlytranslatingthemintotheircorrespondinggenenames.beforeproceedingtoanalysiswithothermorecomprehensiveanalytictools,investigatorscanquicklyglanceatthegenenamestofurthergaininsightabouttheirstudyandtoanswerquestions.DAVIDGeneNameBatchViewerThDAVIDGeneFunctionalclassificationTheFunctionalClassificationToolgeneratesagene-to-genesimilaritymatrixbasedsharedfunctionalannotationusingover75,000termsfrom14functionalannotationsources.Thenovelclusteringalgorithmsclassifieshighlyrelatedgenesintofunctionallyrelatedgroups.DAVIDGeneFunctionalclassifiSimilarityTermOverlap(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,givessharpe