Origin of Co-Expression Patterns in E.coli and S.cerevisiae Emerging from Reverse Engineering Algorithms 英文参考文献.docVIP

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Origin of Co-Expression Patterns in E.coli and S.cerevisiae Emerging from Reverse Engineering Algorithms 英文参考文献.doc

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Origin of Co-Expression Patterns in E.coli and S.cerevisiae Emerging from Reverse Engineering Algorithms 英文参考文献

OriginofCo-ExpressionPatternsinE.coliand S.cerevisiaeEmergingfromReverseEngineering Algorithms MattiaZampieri,NicolaSoranzo,DanieleBianchini,ClaudioAltafini* SISSA-ISAS,InternationalSchoolforAdvancedStudies,Trieste,Italy Abstract Background:Theconceptofreverseengineeringagenenetwork,i.e.,ofinferringagenome-widegraphofputativegene- geneinteractionsfromcompendiaofhighthroughputmicroarraydatahasbeenextensivelyusedinthelastfewyearsto deduce/integrate/validatevarioustypesof‘‘physical’’networksofinteractionsamonggenesorgeneproducts. Results: This paper gives a comprehensive overview of which of these networks emerge significantly when reverse engineeringlargecollectionsofgeneexpressiondatafortwomodelorganisms,E.coliandS.cerevisiae,withoutanyprior information.Forthefirstorganismthepatternofco-expressionisshowntoreflectinfinedetailboththeoperonalstructure oftheDNAandtheregulatoryeffectsexertedbythegeneproductswhenco-participatinginaproteincomplex.Forthe second organism we find that direct transcriptional control (e.g., transcription factor–binding site interactions) has little statistical significance in comparison to the other regulatory mechanisms (such as co-sharing a protein complex, co- localizationonametabolicpathwayorcompartment),whicharehoweverresolvedatalowerlevelofdetailthaninE.coli. Conclusion:Thegeneco-expressionpatternsdeducedfromcompendiaofprofilingexperimentstendtounveilfunctional categories that are mainly associated to stable bindings rather than transient interactions. The inference power of this systematicanalysisissubstantiallyreducedwhenpassingfromE.colitoS.cerevisiae.Thisextensiveanalysisprovidesawayto describe thedifferent complexitybetween the twoorganisms anddiscusses thecritical limitations affecting this type of methodologies. Citation: Zampieri M, Soranzo N,BianchiniD,AltafiniC(2008) Origin ofCo-Expression Patterns in E.coli and S.cerevisiae Emerging fromReverseEngineering Algorithms.PLoSONE3(8):e2981.doi:10.1371/journal.pone.0002981 Editor:Ma