RedeR RBioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations 英文参考文献.docVIP

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RedeR RBioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations 英文参考文献.doc

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RedeR RBioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations 英文参考文献

Castroetal.GenomeBiology2012,13:R29 /2012/13/4/R29 SOFTWARE OpenAccess RedeR:R/Bioconductorpackageforrepresenting modularstructures,nestednetworksandmultiple levelsofhierarchicalassociations MauroAACastro,XinWang,MichaelNCFletcher,KerstinBMeyerandFlorianMarkowetz* Abstract Visualizationandanalysisofmolecularnetworksarebothcentraltosystemsbiology.However,therestillexistsa largetechnologicalgapbetweenthem,especiallywhenassessingmultiplenetworklevelsorhierarchies.Herewe presentRedeR,anR/BioconductorpackagecombinedwithaJavacoreengineforrepresentingmodularnetworks. ThefunctionalityofRedeRisdemonstratedintwodifferentscenarios:hierarchicalandmodularorganizationin geneco-expressionnetworksandnestedstructuresintime-coursegeneexpressionsubnetworks.Ourresults demonstrateRedeRasanewframeworktodealwiththemultiplenetworklevelsthatareinherenttocomplex biologicalsystems.RedeRisavailablefrom/packages/release/bioc/html/RedeR.html. Rationale RedeRisdesignedtodealwiththreekeychallengesin Biological networks contain modules of genes or pro- networkanalysis.Firstly,biologicalnetworksaremodu- teins that may function in the same pathway [1]. As lar and hierarchical, so network visualization needs to genes orproteins inside amodule canbeco-regulated, takeadvantageofsuchstructuralfeaturestoavoidclut- they are often represented by one single node in the tered and uninformative ‘hairballs’. Secondly, network network[2].Suchmodulescanbeinferredbyanumber analysisreliesonstatisticalmethods,manyofwhichare ofstatistical methodsandtheresults areusually repre- alreadyavailableinresourceslikeCRANorBioconduc- sented in graphs [3,4]. Given the complex associations tor.However,themissinglinkbetweenadvancedvisua- that can take place in these graphs, it is a challenge to lization andstatistical computingmakesithardtotake infer and visualize multiple levels orhierarchies within full advantage of R packages for network analysis. andbetweensubnetworkstructures. Thirdly,inlargernetworksuserinp