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1、Dynamicsandcontrolofstate-dependentnetworksSEECOMMENTARYforprobinggenomicorganizationIndikaRajapaksea,b,MarkGroudineb,c,1,andMehranMesbahidaDivisionofBasicSciences,FredHutchinsonCancerResearchCenter,1100FairviewAvenueNorth,Seattle,WA98109;bDepartmentofBiostatisticsandBiomathematics,Pub
2、licHealthSciences,FredHutchinsonCancerResearchCenter,1100FairviewAvenueNorth,Seattle,WA98109;cDepartmentofRadiationOncology,UniversityofWashingtonSchoolofMedicine,Seattle,WA98195;anddDepartmentofAeronauticsandAstronautics,UniversityofWashington,Seattle,WA98195ContributedbyMarkGroudine,
3、August12,2011(sentforreviewJune23,2011)Astate-dependentdynamicnetworkisacollectionofelementsA1thatinteractthroughanetwork,whosegeometryevolvesasBthestateoftheelementschangesovertime.ThegenomeisanFormFunctionintriguingexampleofastate-dependentnetwork,wherechromo-somalgeometrydirectlyrel
4、atestogenomicactivity,whichinturnFormFunctionstronglycorrelateswithgeometry.HereweexaminevariousA2aspectsofagenomicstate-dependentdynamicnetwork.Inparti-cular,weelaborateononeoftheimportantramificationsofFormFunctionviewinggenomicnetworksasbeingstate-dependent,namely,Alignmenttheircont
5、rollabilityduringprocessesofgenomicreorganizationsuchasincelldifferentiation.Timecellulardifferentiation∣cellularreprogramming∣networkcontrollability∣Fig.1.Mechanicsofcellspecialization.(A1,A2,andB)TherelationshipAPPLIEDentropy∣networkorderbetweenspatial(form)andtranscriptional(functio
6、n)networksovertimeMATHEMATICSduringcellspecialization.Alignmentofthenetworks,wherethearchitecturenrecentyears,networksciencehasemergedasapowerfulcon-andtranscriptionalnetworksbecomemutuallyrelated.PriortothealignedIceptualparadigminthebiologicalsciences.Thereasonforthisstate,weproposet
7、wopossiblemodels:(A1)overallcoregulatedgeneistwofold.First,ithasbecomevitaltogainadeeperunderstand-contentemergesaccordingtooverallchromosomeassociations,orformprecedesfunction,and(A2)thetranscriptionalnetworkandcoregulatedingoftheroleofinterelementalinteractionsinthecollectivegenesp
