外文翻译-- An online system for functional relationship.PDF外文翻译-- An online system for functional relationship.PDF

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ANONLINESYSTEMFORFUNCTIONALRELATIONSHIPANALYSISOFGENOMEWIDEGENEPRODUCTSQIANGHU,ZHENGGUOZHANGDEPARTMENTOFBIOMEDICALENGINEERINGINSTITUTEOFBASICMEDICALSCIENCES,CHINESEACADEMYOFMEDICALSCIENCESSCHOOLOFBASICMEDICINE,PEKINGUNIONMEDICALCOLLEGEBEIJING,CHINAEMAILZHANGZG126126COMABSTRACTTHOUGHTHEFUNCTIONALRELATIONSHIPANALYSISFORGENEPRODUCTSISUSEFUL,ACONVENIENTANDUSERFRIENDLYTOOLTOMEASURETHEFUNCTIONALSIMILARITYFORGENOMEWIDEGENEPRODUCTSINMULTIPLESPECIESISSTILLNOTAVAILABLEWECOMPUTEDTHEFUNCTIONALSIMILARITYOFGENEPRODUCTSINGENOMEWIDEINHUMAN,MOUSEANDRATBASEDONOURALGORITHMDATABASEANDWEBSERVICESWEREBUILTBASEDONTHEPRECOMPUTEDSIMILARITYSCORESOURSYSTEMPROVIDEDAGROUPOFTOOLSTORETRIEVETHEFUNCTIONALSIMILARITYANDANALYSISTHEFUNCTIONALRELATIONSHIPFORGENEPRODUCTSTHEWEBSERVICEISFREELYAVAILABLEATHTTP//BMEPUMCEDUCN/FSIM/INDEXHTMLIINTRODUCTIONTHEFUNCTIONALSIMILARITYMEASUREMENTFORGENEPRODUCTSISAUSEFULMETHODTOINVESTIGATETHEIRRELATIONSHIPONEIMPORTANTAPPLICATIONOFFUNCTIONALSIMILARITYANALYSISISTOPREDICTANDASSESSTHEPROTEINPROTEININTERACTIONS1,2,3ANOTHERAPPLICATIONISTODISCOVERTHEPOSITIONALCANDIDATEGENESOFDISEASES4FUNCTIONALSIMILARITYALSOCANBEUSEDTOCLUSTERGENEEXPRESSIONDATAFORFUNCTIONALRELATEDGENESHAVESIMILAREXPRESSIONPROFILES5MOSTOFMETHODSTOMEASUREFUNCTIONALSIMILARITYAREBASEDONTHEANNOTATIONINFORMATIONOFGENEPRODUCTSTHEGENEONTOLOGYGODATABASE6PROVIDESACONTROLLEDVOCABULARYOFTERMSTOANNOTATETHEFUNCTIONSOFGENEPRODUCTSITISWIDELYADOPTEDBYMOSTOFALGORITHMSANDTOOLSTOMEASURETHEFUNCTIONALSIMILARITYTHOUGHMANYTOOLSHAVEBEENDEVELOPEDTOMEASURETHEFUNCTIONALSIMILARITY,ACONVENIENTANDUSERFRIENDLYTOOLTOANALYSISTHERELATIONSHIPOFGENOMEWIDEGENEPRODUCTSISSTILLNOTAVAILABLETHEGOTOOLSWEBPAGECOLLECTEDALOTOFSOFTWAREBASEDONTHEDATABASEFOREXAMPLE,AMIGO7ANDQUICKGO8PROVIDEANINTERFACETOSEARCHANDBROWSETHEONTOLOGYANDANNOTATIONDATATHERELATIONSHIPOFGENEPRODUCTSCANBECOMPAREDBYUSERSBUTNOTAUTOMATICALLYGOTAX9THATINTEGRATEDTHEANNOTATIONDATAOFPROTEINANDPROTEINFAMILIESPROVIDEDAFUNCTIONALSIMILARITYSEARCHTOOLFSSTBASEDONTHEALGORITHMOFINFORMATIONCONTENTICOFGOTERMSTHETOOLCANBEUSEDTOMEASURETHEFUNCTIONALSIMILARITYOFPROTEINSANDPROTEINFAMILIESGSESAME10DEVELOPEDANEWALGORITHMTOMEASURETHEFUNCTIONALSIMILARITYTHEWEBTOOLITOFFEREDONLYCANBEUSEDTOMEASURETHEFUNCTIONALSIMILARITYOFTWOGENEPRODUCTSFUNSIMMAT11CALCULATEDTHESIMILARITYOFPROTEINSINUNIPROTKB12AWEBSEARCHENGINEWASDEVELOPEDTORETRIEVETHEFUNCTIONALSIMILARITYOFPROTEINSITWOULDBEHELPFULIFATOOLCOULDASSISTBIOLOGISTSTOCOMPARETHEFUNCTIONALRELATIONSHIPOFINTERESTEDGENESWITHWHOLEGENOMEGENEPRODUCTSHOWEVER,GENOMEWIDERELATIONSHIPANALYSISCOULDNOTBECARRIEDOUTINORDINARYCOMPUTINGSERVERSITWOULDCOSTDOZENSOFHOURSEVENINHIGHPERFORMANCECLUSTERWEDEVELOPEDANONLINESYSTEMFORFUNCTIONALRELATIONSHIPANALYSISOFGENOMEWIDEGENEPRODUCTSANALLAGAINSTALLFUNCTIONALSIMILARITYCOMPARISONFORGENOMEWIDEGENEPRODUCTSINHUMAN,MOUSEANDRATWERECOMPUTEDPRELIMINARILYBASEDONOURALGORITHMSTHREEDATABASESWEREBUILTTOINTEGRATETHESIMILARITYSCORESRESPECTIVELYBASEDONTHEPRECOMPUTEDSIMILARITYSCORES,AWEBSEARCHENGINEWASDEVELOPEDTORETRIEVETHESIMILARITYSCORESDIRECLTYSOMEOTHERRELATEDTOOLSWEREDEVELOPEDTOEXTENDTHEONLINEWEBSERVICESBIOLOGISTSCANUSETHESYSTEMEASILYTOANALYZETHEFUNCTIONALRELATIONSHIPOFGENOMEWIDEGENEPRODUCTSIICONSTRUCTIONANDCONTENTADATASETSTHERAWDATAADOPTEDTOCALCULATETHESIMILARITYWEREDIRECTLYFROMTHEANNOTATIONPACKAGESOFR/BIOCONDUCTORPROJECT13,14FOREXAMPLE,THEPACKAGESORGHSEGDB,ORGMMEGDBANDORGRNEGDBCONTAINEDTHEGOANNOTATIONDATAOFGENEPRODUCTSINHUMAN,MOUSEANDRATRESPECTIVELYTHEPACKAGESWEREDESCRIBEDINTHETABLEIALLTHESEGORELATEDPACKAGESWEREBUILTBYBIOCONDUCTORPROJECTACCORDINGTOTHELATESTVERSIONOFGODATABASEIN2009MARCHTHEANNOTATIONDATAOFPROBEIDSOFDIFFERENTMICROARRAYPLATFORMSWEREALSOFROMTHEANNOTATIONPACKAGESINBIOCONDUCTORBIMPLEMENT1ALGORITHMTHREEDATABASESINTEGRATEDALLSIMILARITYSCORESOFGENOMEWIDEGENEPRODUCTSINHUMAN,MOUSEANDRATRESPECTIVELYWEPROPOSEDANOVELALGORITHMTOMEASURETHERELATIONSHIPSTATISTICALMODELWASBUILTACCORDINGTOTHECOMMONINFORMATIONOFTHEANNOTATIONTERMSBETWEENTWOGENEPRODUCTSTHEGOPROVIDEDTHREESTRUCTUREDVOCABULARIESONTOLOGIESTODESCRIBEGENEPRODUCTSINTERMSOFTHEIRASSOCIATEDBIOLOGICALPROCESSESBP,CELLULARCOMPONENTS9781424447138/10/25002010IEEEFIG1FUNCTIONALSIMILARITYSEARCHFORGENEPRODUCTSTABLEIDATASETSADOPTEDINTHEDATABASESANNOTATIONPACKAGESSPIECESRAWDATAORGHSEGDBHUMANGOANNOTATION;MAPPINGINFORMATIONBETWEENDISTINCTIDENTIFICATIONSORGMMEGDBMOUSEDITTOORGRNEGDBRATDITTOORGHSSPDBHUMANPROTEINIDENTIFIERSTOENTREZIDSORGMMSPDBMOUSEDITTOORGRNSPDBRATDITTOGODBGOTERMSRELATIONSHIPANDANNOTATIONKEGGDBANNOTATIONMAPSFORKEGGDATABASECCANDMOLECULARFUNCTIONSMFTHEGOTERMSCOULDBECONNECTEDWITHCHILDPARENTRELATIONSHIPBETWEENEACHOTHERTHETHREEONTOLOGIESWERESTRUCTUREDASDIRECTEDACYCLICGRAPHDAGGOTERMSWEREINDIFFERENTLEVELSOFTHEDAGTHETERMSLOCATEDCLOSETOTHELEAVESOFDAGDESCRIBEDMORESPECIFICMEANINGSTHESETERMSCONTAINEDMOREINFORMATIONTHANTHETERMSLOCATEDCLOSETOTHEROOTWEDEFINEDAPARAMETER,LEVELCOEFFICIENTLC,TODENOTETHEWEIGHTOFTHEINFORMATIONOFAGOTERMTHELCVALUESOFLEAVESWEREDEFINEDAS1FROMCHILDRENTOPARENTS,THELCVALUESGRADUALLYDECREASEDASTHERATIOOFTHEIRLEVELSINTHEDAGAGENEUSUALLYWASANNOTATEDBYMOR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编号:201311191259373759    类型:共享资源    大小:269.92KB    格式:PDF    上传时间:2013-11-19
  
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