Systems Biology for Signaling Networks

900 Pages·2010·31.558 MB·English

by  Sangdun Choi (auth.), Sangdun Choi (eds.)

Sangdun Choi
Editor
Systems Biology
for Signaling Networks
123
Editor
SangdunChoi
DepartmentofMolecularScience
andTechnology
DepartmentofBiologicalScience
CollegeofNaturalScience
AjouUniversity
442-749Suwon
Korea,Republicof(SouthKorea)
[email protected]
ISBN978-1-4419-5796-2 e-ISBN978-1-4419-5797-9
DOI10.1007/978-1-4419-5797-9
SpringerNewYorkDordrechtHeidelbergLondon
LibraryofCongressControlNumber:2010932192
©SpringerScience+BusinessMedia,LLC2010
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Preface
Systems biology is a recently emerged academic field that aims to understand the
relationshipsfromgenestoorganismsthroughnetworksinbiologicalsystems.The
vastamountofdatacurrentlybeinggeneratedshouldbeaddressedinameaningful
way,andthedevelopmentofsystematicapproachesmayleadtoanewapproachto
scientificstudy.Sincetheyear2000,theterm“SystemsBiology”hasbeenwidely
usedinbiosciences,buttheactualprocesshasnotyetbeenwelldefined.Therefore,I
havecreatedabookseriestodescribesystemsbiologyinconjunctionwithSpringer
(http://www.springer.com).
The current book, Systems Biology for Signaling Networks, is part of a series
(serieseditor:SangdunChoi)consistingof
1. SystemsBiologyforSignalingNetworks(ChoiS)
2. SystemsImmunology(SelvarajooKandTsuchiyaM)
3. Physiologic Computer Modeling and Systems Analysis for the Clinical
Researcher(SummersRLandColemanTG)
4. SystemsBiologyofRegulatedExocytosisinPancreaticβ-Cells(Booß-Bavnbek
B,KlösgenB,LarsenJK,PociotFandRenströmE)
Thescopeofthisseriesofbooksiswideandrangesfromthemolecularpartsof
cellstonetworkmodeling.Amongthem,SystemsBiologyforSignalingNetworks
focuses on systematic approaches to cellular signaling in humans and animals.
Although systems biology is in its infancy, our book offers an exciting solution in
termsofexploringcellularsignalingthatwillbeagreathelptobiomedicalstudies
inthiscentury.
Suwon,Korea SangdunChoi
v

Contents
PartI Concepts
1 SystemsBiologyApproaches:SolvingNewPuzzlesina
SymphonicManner . . . . . . . . . . . . . . . . . . . . . . . . . . 3
SangdunChoi
2 Current Progress inStaticand Dynamic Modeling of
BiologicalNetworks . . . . . . . . . . . . . . . . . . . . . . . . . . 13
BernieJ.Daigle,Jr.,BalajiS.Srinivasan,JasonA.Flannick,
AntalF.Novak,andSerafimBatzoglou
3 GettingStartedinBiologicalPathwayConstruction . . . . . . . . 75
RebeccaA.SealfonandStuartC.Sealfon
4 FromMicroarraytoBiology . . . . . . . . . . . . . . . . . . . . . 85
MikhailDozmorovandRobertE.Hurst
PartII ModelingandReconstruction
5 ComputationalProceduresforModelIdentification . . . . . . . . 111
EvaBalsa-CantoandJulioR.Banga
6 AssemblyofLogic-BasedDiagramsofBiologicalPathways . . . . 139
TomC.Freeman
7 Automating Mathematical Modeling of Biochemical
ReactionNetworks . . . . . . . . . . . . . . . . . . . . . . . . . . 159
AndreasDräger,AdrianSchröder,andAndreasZell
8 StrategiestoInvestigateSignalTransductionPathways
withMathematicalModelling . . . . . . . . . . . . . . . . . . . . 207
JulioVera,SvetoslavNikolov,andOlafWolkenhauer
9 InferringTranscriptionalRegulatoryNetwork . . . . . . . . . . . 235
MingZhan
10 FindingFunctionalModules . . . . . . . . . . . . . . . . . . . . . 253
MutluMete,FushengTang,XiaoweiXu,andNurcanYuruk
vii
viii Contents
11 ModelingtheDynamicsofBiologicalNetworksfromTime
CourseData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
SašoDžeroskiandLjupcˇoTodorovski
12 DecisionMakinginCells . . . . . . . . . . . . . . . . . . . . . . . 295
TomášHelikar,NaomiKochi,JohnKonvalina,and
JimA.Rogers
13 RobustnessofNeuralNetworkModels . . . . . . . . . . . . . . . 337
DanielW.FranksandGraemeD.Ruxton
14 FunctionalModulesinProtein–ProteinInteractionNetworks . . 353
TobiasMüllerandMarcusDittrich
15 MixtureModelonGraphs:AProbabilisticModelfor
Network-BasedAnalysisofProteomicData. . . . . . . . . . . . . 371
JosselinNoirel,GuidoSanguinetti,andPhillipC.Wright
16 IntegrationofNetworkInformationforProteinFunction
Prediction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 399
XiaoyuJiangandEricD.Kolaczyk
PartIII ApplicationsforSignalingNetworks
17 Cellular-Level Gene Regulatory Networks: Their
DerivationandProperties . . . . . . . . . . . . . . . . . . . . . . 429
BenjamindeBivort
18 Tyrosine-PhosphoproteomeDynamics . . . . . . . . . . . . . . . . 447
MasaakiOyama,ShinyaTasaki,andHirokoKozuka-Hata
19 SystemsBiologyoftheMAPK1,2Network . . . . . . . . . . . . . 455
MelissaMullerandPrahladT.Ram
20 PathwayCrosstalkNetwork . . . . . . . . . . . . . . . . . . . . . 491
YongLi
21 CrosstalkBetweenMitogen-ActivatedProteinKinase
andPhosphoinositide-3KinaseSignalingPathwaysin
DevelopmentandDisease . . . . . . . . . . . . . . . . . . . . . . . 505
JijunHao,MarieA.Daleo,andCharlesC.Hong
22 Systems-Level Analyses of the Mammalian Innate
ImmuneResponse . . . . . . . . . . . . . . . . . . . . . . . . . . . 531
DavidJ.Lynn,JenniferL.Gardy,ChristopherD.Fjell,
RobertE.W.Hancock,andFionaS.L.Brinkman
23 Molecular Basis of Protective Anti-Inflammatory
SignallingbyCyclicAMPintheVascularEndothelium . . . . . . 561
ClaireRutherfordandTimothyM.Palmer
Contents ix
24 Construction of Cancer-Perturbed Protein–Protein
InteractionNetworkofApoptosisforDrugTargetDiscovery . . . 589
Liang-HuiChuandBor-SenChen
25 TranscriptionalChangesinAlzheimer’sDisease . . . . . . . . . . 611
JeremyA.MillerandDanielH.Geschwind
26 PathogenesisofObesity-RelatedChronicLiverDiseases
astheStudyCasefortheSystemsBiology . . . . . . . . . . . . . 645
AnchaBaranova,AybikeBirerdinc,MichaelEstep,and
ZobairM.Younossi
27 TheEvolvingTranscriptomeofHeadandNeckSquamous
CellCarcinoma . . . . . . . . . . . . . . . . . . . . . . . . . . . . 687
Yau-HuaYu
28 PeptideMicroarraysforaNetworkAnalysisofChanges
inMolecularInteractionsinCellularSignalling . . . . . . . . . . 703
MichaelD.SinzingerandRolandBrock
PartIV ToolsforSystemsBiology
29 APrimeronModularMass-ActionModellingwithCellML . . . 721
MichaelT.Cooling
30 FERN–StochasticSimulationandEvaluationofReaction
Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 751
FlorianErhard,CarolineC.Friedel,andRalfZimmer
31 ProgrammingBiologyinBlenX . . . . . . . . . . . . . . . . . . . 777
LorenzoDematté,RobertoLarcher,AlidaPalmisano,
CorradoPriami,andAlessandroRomanel
32 DiscreteModelling:PetriNetandLogicalApproaches . . . . . . 821
InaKochandClaudineChaouiya
33 ProteoLens:ADatabase-DrivenVisualDataMiningTool
forNetworkBiology . . . . . . . . . . . . . . . . . . . . . . . . . . 857
JakeYueChenandTianxiaoHuan
34 MADNet:AWebServerforContextualAnalysisand
VisualizationofHigh-ThroughputExperiments . . . . . . . . . . 877
IgorŠegota,PetarGlažar,andKristianVlahovicˇek
SubjectIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 889

Contributors
EvaBalsa-Canto (Bio)ProcessEngineeringGroup,IIM-CSIC(SpanishNational
ResearchCouncil),C/EduardoCabello,6,36208-Vigo,Spain,[email protected]
JulioR.Banga (Bio)ProcessEngineeringGroup,IIM-CSIC(SpanishNational
ResearchCouncil),C/EduardoCabello,6,36208-Vigo,Spain
AnchaBaranova CenterfortheStudyofGenomicsinLiverDiseases,Molecular
andMicrobiologyDepartment,GeorgeMasonUniversity,Fairfax,Virginia,USA,
[email protected]
SerafimBatzoglou DepartmentofComputerScience,StanfordUniversity,
Stanford,CA,USA,serafi[email protected]
AybikeBirerdinc CenterfortheStudyofGenomicsinLiverDiseases,Molecular
andMicrobiologyDepartment,GeorgeMasonUniversity,Fairfax,Virginia,USA,
[email protected]
FionaS.L.Brinkman DepartmentofMolecularBiologyandBiochemistry,8888
UniversityDrive,SimonFraserUniversity,Burnaby,BritishColumbia,Canada,
V5A1S6
RolandBrock DepatmentofBiochemistry,NijmegenCentreforMolecularLife
Sciences,RadboudUniversityNijmegenMedicalCentre,Nijmegen,The
Netherlands,[email protected]
ClaudineChaouiya IGC,InstitutoGulbenkiandeCiência,RuadaQuintaGrande
6,P-2780-156Oeiras,Portugal,[email protected]
Bor-SenChen DepartmentofElectricalEngineering,NationalTsingHua
University,101,Section2,Kuang-FuRoad,Hsinchu30013,Taiwan,
[email protected]
JakeYueChen IndianaUniversitySchoolofInformatics;Departmentof
Computer&InformationScience,PurdueUniversity;IndianaCenterforSystems
BiologyandPersonalizedMedicine,WK190,719IndianaAVE,Indianapolis,IN
46209,USA,[email protected]
xi
xii Contributors
Liang-HuiChu DepartmentofElectricalEngineering,NationalTsingHua
University,101,Section2,Kuang-FuRoad,Hsinchu30013,Taiwan,
[email protected]
SangdunChoi DepartmentofMolecularScienceandTechnology,Ajou
University,Suwon,443-749,korea,[email protected]
MichaelT.Cooling AucklandBioengineeringInstitute,UniversityofAuckland,
Auckland,NewZealand,[email protected]
BernieJ.Daigle,Jr. DepartmentofGenetics,StanfordUniversitySchoolof
Medicine,Stanford,CA,USA,[email protected]
MarieA.Daleo DepartmentofMedicine,DivisionofCardiovascularMedicine,
DepartmentofPharmacology,VanderbiltUniversitySchoolofMedicine,
Nashville,TN,USA,[email protected]
BenjamindeBivort RowlandInstituteatHarvard,HarvardUniversity,100
EdwinLandBlvd,Cambridge,MA02142,USA,[email protected]
LorenzoDematté CoSBiandUniversitàdiTrento,Trento,Italy
MarcusDittrich Biocenter,BioinformaticsDepartment,UniversityofWuerzburg,
97074Wuerzburg,Germany,[email protected]
MikhailDozmorov DepartmentsofUrology,OklahomaUniversityHealth
SciencesCenter,OklahomaCity,OK,73104,USA
AndreasDräger CenterforBioinformaticsTübingen(ZBIT),Sand1,72076
Tübingen,UniversityofTübingen,Germany,[email protected]
SašoDžeroski DepartmentofKnowledgeTechnologies,JožefStefanInstitute,
Jamova39,SI-1000Ljubljana,slovenia,[email protected]
FlorianErhard LFEBioinformatik,InstitutfürInformatik,
Ludwig-Maximilians-UniversitätMünchen,Amalienstraße,17,80333M¨unchen,
Germany,fl[email protected]fi.lmu.de
MichaelEstep BettyandGuyBeattyCenterforIntegratedResearch,Inova
HealthSystem,FallsChurch,Virginia,USA,[email protected]
ChristopherD.Fjell CentreforMicrobialDiseasesandImmunityResearch,
232-2259LowerMall,UniversityofBritishColumbia,Vancouver,British
Columbia,Canada,V6T1Z4
JasonA.Flannick MedicalandPopulationGenetics,TheBroadInstituteof
HarvardandMIT,Cambridge,MA,fl[email protected]
DanielW.Franks YorkCentreforComplexSystemsAnalysis(YCCSA),
DepartmentofBiology,andDepartmentofComputerScience,UniversityofYork,
YO105YW,UK,[email protected]