12clustering

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1、Biochem218-2010Lecture12ClusteringandFunctionalAnalysisofCoordinatelyRegulatedGenes!GavinSherlock!sherlock@genome.stanford.edu!February11th2010!ClusteringCoordinatelyRegulatedGenes•Whatarethegoalsoftypicalexpressionexperiments?!•Howcanwedetermineiftwogen

2、esare‘coexpressed’?!•Whatcanweinferwhenwedecidethattwogenesarecoexpressed?!VisualizingDataMAK16YAL025C5MAK160.5YBL015WACH14YBL048W0OD0.26OD0.46OD0.80OD1.80OD3.70OD6.90OD7.30YBL048W3YBL049WYBL049W2-0.5YBL064CYBL064C1YBL078CYBL078C-1MAK160YBR072WHSP26-1YBR

3、139W-1.5YBR139WOD0.26OD0.46OD0.80OD1.80OD3.70OD6.90OD7.30YBR147W-2YBR147W-2YCR021C-3HSP30YDL085W-4YDL085W-2.5YDL204WYDL204WYDL208WNHP2ExtractingDataExperiments2001000050.005.64480048001.000.00Genes90003000.03-4.91Cy5⎛Cy5⎞log⎜⎜⎟⎟Cy3Cy52Cy3⎝Cy3⎠Visualizing

4、Data(cont.)ExpressionDuringSporulation5Series1Series2Series3Series44Series5Series6Series7Series8Series9Series103Series11Series12Series13Series14Series152Series16Series17Series18Series19Series20Series211Series22Series23Series24Series25Series26LogRatio0Ser

5、ies270246810Series28Series29Series30Series31-1Series32Series33Series34Series35Series36Series37-2Series38Series39Series40Series41Series42-3Series43Series44Series45Series46Series47-4Series48Series49Time(hours)Series50Series51OrganizingDataInmicroarraystudi

6、es,weoftenuseclusteringalgorithmstohelpusidentifypatternsincomplexdata.Forexample,wecanrandomizethedatausedtorepresentthispaintingandseeifclusteringwillhelpusvisualizethepattern.ClusteringalgorithmsFirst,werepresentthepaintinginblackandwhite.Clusteringal

7、gorithmsThepaintingis“sliced”intorowswhicharethenrandomized.ClusteringalgorithmsRowsorderedbyhierarchicalclusteringwithnodesflippedtooptimizeorderingClusteringalgorithmsRowsorderedbyusingaSelf-OrganizingMap(SOM)!Randomvs.BiologicalDataFromEisenMB,etal,PN

8、AS199895(25):14863-8GoalofClustering!Value2Value1!TypesofClustering•Agglomerative!–Bottomupapproach!–Differentvariantsofhierarchicalclustering!–Thisisthetypicalclusteringyousee!•Partitioning/Divisive!–Topdownapproach!–K-me