蛋白质GeneontologyKEGG分析软件David使用方法介绍课件.ppt

蛋白质GeneontologyKEGG分析软件David使用方法介绍课件.ppt

《蛋白质GeneontologyKEGG分析软件David使用方法介绍课件.ppt》由会员分享，可在线阅读，更多相关《蛋白质GeneontologyKEGG分析软件David使用方法介绍课件.ppt（29页珍藏版）》请在冰豆网上搜索。

DAVID,DatabaseforAnnotation,VisualizationandIntegratedDiscovery,DAVIDprovidesacomprehensivesetoffunctionalannotationtoolsforinvestigatorstounderstandbiologicalmeaningbehindlargelistofgenes,Identifyenrichedbiologicalthemes,particularlyGOtermsDiscoverenrichedfunctional-relatedgenegroupsClusterredundantannotationtermsVisualizegenesonBioCarta&KEGGpathwaymapsDisplayrelatedmany-genes-to-many-termson2-Dview.SearchforotherfunctionallyrelatedgenesnotinthelistListinteractingproteinsExploregenenamesinbatchLinkgene-diseaseassociationsHighlightproteinfunctionaldomainsandmotifsRedirecttorelatedliteraturesConvertgeneidentifiersfromonetypetoanother.,GeneListManager,DAVIDAnalyticModules,Anygivengeneisassociatingwithasetofannotationterms.Ifgenessharesimilarsetofthoseterms,theyaremostlikelyinvolvedinsimilarbiologicalmechanisms.Thealgorithmadoptskappastatisticstoquantitativelymeasurethedegreeoftheagreementhowgenessharethesimilarannotationterms.Kapparesultrangesfrom0to1.ThehigherthevalueofKappa,thestrongertheagreement.Kappamorethan0.7typicallyindicatesthatagreementoftwogenesarestrong.Kappavaluesgreaterthan0.9areconsideredexcellent.,ParameterPanel,GeneClustersIdentifiedbyDAVID,UsersgeneIDs&Names,1,2,Viewandselectannotationcategoriesofyourinterests,3,3,3,Percentage,e.g.44/163,Genesfromthelistinvolvedinthisannotationcategory,SinglechartreportonlyforthisAnnotationcategories,TablereportforallSelectedannotationcategories,Linearorredundantchartreportofannotationtermsforallselectedannotationcategoriesabove,Clusteredornon-redundantchartreportofannotationtermsforallselectedannotationcategoriesabove,DAVIDGeneIDConversionTool（DGCT）,Ifasignificantportion（20%）ofinputgeneIDsfailtobemappedtoaninternalDAVIDID,aspeciallydesignedmodule,theDAVIDGeneIDConversionTool,willstartuptohelpmapsuchIDs.,DAVIDGeneNameBatchViewer,ThegenenamebatchviewerisabletoquicklyattachmeaningtoalistofgeneIDsbyrapidlytranslatingthemintotheircorrespondinggenenames.beforeproceedingtoanalysiswithothermorecomprehensiveanalytictools,investigatorscanquicklyglanceatthegenenamestofurthergaininsightabouttheirstudyandtoanswerquestions.,DAVIDGeneFunctionalclassification,TheFunctionalClassificationToolgeneratesagene-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.,