Gene Network Landscape of the Ciliate Tetrahymena thermophila 英文参考文献.docVIP

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Gene Network Landscape of the Ciliate Tetrahymena thermophila 英文参考文献.doc

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Gene Network Landscape of the Ciliate Tetrahymena thermophila 英文参考文献

GeneNetworkLandscapeoftheCiliateTetrahymena thermophila JieXiong1,2,DongxiaYuan1,3.,JeffreyS.Fillingham4.,JyotiGarg5.,XingyiLu1,2,YueChang1,2 ,Yifan Liu6,ChengjieFu1,RonaldE.Pearlman5,WeiMiao1* 1Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China, 2Graduate School of Chinese AcademyofSciences,Beijing,China,3StateKeyLaboratoryofFreshwaterEcologyandBiotechnology,InstituteofHydrobiology,ChineseAcademyofSciences,Wuhan, China,4DepartmentofChemistryandBiology,RyersonUniversity,Toronto,Ontario,Canada,5DepartmentofBiologyandCenterforResearchinMassSpectrometry, YorkUniversity,Toronto,Ontario,Canada,6PathologyDepartment,UniversityofMichiganMedicalSchool,AnnArbor,Michigan,UnitedStatesofAmerica Abstract Background:Genome-wideexpressiondataofgenemicroarrayscanbeusedtoinfergenenetworks.Atacellularlevel,a genenetworkprovidesapictureofthemodulesinwhichgenesaredenselyconnected,andofthehubgenes,whichare highly connected with other genes. A gene network is useful to identify the genes involved in the same pathway, in a protein complex or that are co-regulated. In this study, we used different methods to find gene networks in the ciliate Tetrahymenathermophila,anddescribesomeimportantpropertiesofthisnetwork,suchasmodulesandhubs. Methodology/Principal Findings: Using 67 single channel microarrays, we constructed the Tetrahymena gene network (TGN)usingthreemethods:thePearsoncorrelationcoefficient(PCC),theSpearmancorrelationcoefficient(SCC)andthe contextlikelihoodofrelatedness(CLR)algorithm.Theaccuracyandcoverageofthethreenetworkswereevaluatedusing fourconservedproteincomplexesinyeast.TheCLRnetworkwithaZ-scorethreshold3.49wasdeterminedtobethemost robust.TheTGNwaspartitioned,and55moduleswerefound.Inaddition,analysisofthearbitrarilydetermined1200hubs showedthatthesehubscouldbesortedintosixgroupsaccordingtotheirexpressionprofiles.Wealsoinvestigatedhuman diseaseorthologsinTetrahymenathataremissinginyeastandprovideevid