Gene Ontology Analysis基因本体论分析解析.pdf

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1、Lecture21GeneOntologyAnalysisMCB416A/516AStatisticalBioinformaticsandGenomicAnalysisProf.LinglingAnUnivofArizonaLasttime:RcodeforclusteranalysisWhyneeddoscaling?Advancedheatmap2OutlineIntroductiontoGeneOntologyGenesetenrichment3Afterdetectsignif

2、icantgenesindifferentialexpressionanalysis…Dataonngenesformhybridizationsresultsinanxmgene-by-arraydatamatrixArray1Array2Array3Array4Array5…Gene10.460.300.801.510.90...Gene2-0.100.490.240.060.46...Gene30.150.740.040.100.20...Gene4-0.45-1.03-0.79-0.56

3、-0.32...Gene5-0.061.061.351.09-1.09...………………...Preprocessing->normalization->summarization->testing=>Listofdifferentiallyexpressedgenes4Howtointerpretethedata?Drivenbyexperimentalquestions,butwithalonglistofsiginficantgeneswhichgenesareofinterest?

4、what’sspecialaboutthedifferentiallyexpressedgenes?Solution:poolingofgenesintofunctionalclassesprovidesageneraloverviewGeneOntologydatabaseprovidessuchafunctionalclassification5Afterclusteringgenes,thenwhat?Assign(orhypothesizeabout)biologicalmean

5、ingstoclustersIdentifyover-representedfunctionalcategoriesintheclusters(i.e.,clustermaycontainmoregenesknowntobeinvolvedinaspecificbiologicalprocessthanwouldbeexpectedbychance)Ifyoufindageneofunknownfunctioninaclusterofgenesinwhichaknownfunctioniso

6、verrepresented,yourgeneofunknownfunctionmayhavethesameorarelatedfunction!Requirementsforsystematicanalysis:StandardassignmentofgenesintofunctionalcategoriesControlledvocabularyfordescribingbiologicalmeaningsGeneOntologyorGOprojectatNCBI6GeneOntol

7、ogyOntology:AstructuredvocabularydescribesconceptsthatexistinanareaofknowledgedescribesrelationshipsthatexistbetweenthemGeneOntology(GO):describespossiblefunctionsofgenesdescribesrelationshipsbetweengenesGOisindependentoftheorganismsomefunctions

8、arecommontomanyorganismssomeareorganism-specific7GOisapublicresource8GeneOntology(GO)projecthttp://www.geneontology.org/Purpose:1)Establishaunifiedframeworkfororganism-independentgeneannotation2)Definecontrolledterms(ontologies)fordescriptionofgene