Analyzing Network Data in Biology and Medicine: An Interdisciplinary Textbook for Biological, Medical and Computational Scientists

648 Pages·2019·25.942 MB·English

by  Nataša Pržulj (Editor)

Analyzing Network Data in Biology and Medicine
AnInterdisciplinaryTextbookforBiological,Medical,
andComputationalScientists
The increased and widespread availability of large network data resources in recent
yearshasresultedinagrowingneedforeffectivemethodsfortheiranalysis.Thechal-
lengeistodetectpatternsthatprovideabetterunderstandingofthedata.However,
thisisnotastraightforwardtaskbecauseofthesizeofthedatasetsandthecomputer
powerrequiredfortheanalysis.Thesolutionistodevisemethodsforapproximately
answeringthequestionsposedandthesemethodswillvarydependingonthedatasets
underscrutiny.Thiscutting-edgetextintroducesbiologicalconceptsandbiotechnolo-
gies producing the data, graph and network theory, cluster analysis and machine
learning,beforediscussingthethoughtprocessesandcreativityinvolvedintheanal-
ysis of large-scale biological and medical datasets, using a wide range of real-life
examples.Bringingtogetherleadingexperts,thistextprovidesanidealintroduction
toandinsightintotheinterdisciplinaryfieldofnetworkdataanalysisinbiomedicine.
Natasˇa Przˇulj is Professor of BiomedicalDataScience at University CollegeLondon
(UCL) and an ICREA Research Professor at Barcelona Supercomputing Center. She
has been an elected academician of The Academy of Europe, Academia Europaea,
since 2017 and is a Fellow of the British Computer Society (BCS). She is recognized
for designing methods to mine large real-world molecular network datasets and
for extending and using machine learning methods for integration of heteroge-
neous biomedical and molecular data, applied to advancing biological and medical
knowledge.ShereceivedtwoprestigiousEuropeanResearchCouncil(ERC)research
grants,Starting(2012–2017)andConsolidator(2018–2023),andUSANationalScience
Foundation(NSF)grantsamongothers.SheisarecipientoftheBCSRogerNeedham
Award for 2014. She was previously an Associate Professor (Reader, 2012–2016) and
AssistantProfessor(Lecturer,2009–2012)intheDepartmentofComputingatImperial
College London and an Assistant Professor in the Computer Science Department at
UniversityofCaliforniaIrvine(2005–2009).SheobtainedaPhDinComputerScience
fromUniversityofTorontoin2005.

Analyzing Network
Data in Biology and
Medicine
An Interdisciplinary Textbook for Biological,
Medical, and Computational Scientists
Editedandauthoredby
NATASˇA PRZˇ ULJ
ProfessorofBiomedicalDataScience,ComputerScienceDepartment,
UniversityCollegeLondon
ICREAResearchProfessoratBarcelonaSupercomputingCenter
UniversityPrintingHouse,CambridgeCB28BS,UnitedKingdom
OneLibertyPlaza,20thFloor,NewYork,NY10006,USA
477WilliamstownRoad,PortMelbourne,VIC3207,Australia
314-321,3rdFloor,Plot3,SplendorForum,JasolaDistrictCentre,
NewDelhi–110025,India
79AnsonRoad,#06–04/06,Singapore079906
CambridgeUniversityPressispartoftheUniversityofCambridge.
ItfurtherstheUniversity’smissionbydisseminatingknowledgeinthepursuitof
education,learning,andresearchatthehighestinternationallevelsofexcellence.
www.cambridge.org
Informationonthistitle:www.cambridge.org/bionetworks
DOI:10.1017/9781108377706
©CambridgeUniversityPress2019
Thispublicationisincopyright.Subjecttostatutoryexception
andtotheprovisionsofrelevantcollectivelicensingagreements,
noreproductionofanypartmaytakeplacewithoutthewritten
permissionofCambridgeUniversityPress.
Firstpublished2019
PrintedandboundinGreatBritainbyClaysLtd,ElcografS.p.A.
AcataloguerecordforthispublicationisavailablefromtheBritishLibrary.
LibraryofCongressCataloging-in-PublicationData
Names:Przˇulj,Natasˇa,editor.
Title:Analyzingnetworkdatainbiologyandmedicine:aninterdisciplinary
textbookforbiological,medicalandcomputationalscientists/editedby
NatasˇaPrzˇulj,UniversityCollegeLondon.
Description:Cambridge,UnitedKingdom;NewYork,NY:CambridgeUniversity
Press,2019.|Includesbibliographicalreferences.
Identifiers:LCCN2018034214|ISBN9781108432238(hardback:alk.paper)
Subjects:LCSH:Medicalinformatics–Dataprocessing.|Bioinformatics.
Classification:LCCR858.A4692019|DDC610.285–dc23
LCrecordavailableathttps://lccn.loc.gov/2018034214
ISBN978-1-108-43223-8Paperback
Additionalresourcesforthispublicationatwww.cambridge.org/bionetworks
CambridgeUniversityPresshasnoresponsibilityforthepersistenceoraccuracy
ofURLsforexternalorthird-partyinternetwebsitesreferredtointhispublication
anddoesnotguaranteethatanycontentonsuchwebsitesis,orwillremain,
accurateorappropriate.
Tomylovingfamily:Cvita,Bogdan,Nina,Sofia,andLaurentino.
Andtomybestfriend,Vesna.

Contents
ListofContributors pageix
Preface xiii
1 FromGeneticDatatoMedicine:FromDNASamplestoDiseaseRiskPrediction
inPersonalizedGeneticTests 1
LUISG.LEAL,ROKKOSˇIR,ANDNATASˇAPRZˇULJ
2 EpigeneticDataandDisease 63
RODRIGOGONZALEZ-BARRIOS,MARISOLSALGADO-ALBARRA´N,NICOLA´S
ALCARAZ,CRISTIANARRIAGA-CANON,LISSANIAGUERRA-CALDERAS,
LAURACONTRERAS-ESPINOSA,ANDERNESTOSOTO-REYES
3 IntroductiontoGraphandNetworkTheory 111
THOMASGAUDELETANDNATASˇAPRZˇULJ
4 Protein–ProteinInteractionData,theirQuality,andMajorPublic
Databases 151
ANNE-CHRISTINHAUSCHILD,CHIARAPASTRELLO,MAXKOTLYAR,
ANDIGORJURISICA
5 GraphletsinNetworkScienceandComputationalBiology 193
KHALIQUENEWAZANDTIJANAMILENKOVIC´
6 UnsupervisedLearning:ClusterAnalysis 241
RICHARDRO¨TTGER
7 MachineLearningforDataIntegrationinCancerPrecisionMedicine:Matrix
FactorizationApproaches 286
NOE¨LMALOD-DOGNIN,SAMF.L.WINDELS,AND
NATASˇAPRZˇULJ
8 MachineLearningforBiomarkerDiscovery:SignificantPatternMining 313
FELIPELLINARES-LO´PEZANDKARSTENBORGWARDT
9 NetworkAlignment 369
NOE¨LMALOD-DOGNINANDNATASˇAPRZˇULJ
10 NetworkMedicine 414
PISANUBUPHAMALAI,MICHAELCALDERA,FELIXMU¨LLER,
ANDJO¨RGMENCHE
11 ElucidatingGenotype-to-PhenotypeRelationshipsviaAnalysesofHuman
TissueInteractomes 459
IDANHEKSELMAN,MORANSHARON,OMERBASHA,ANDESTI
YEGER-LOTEM
vii
viii CONTENTS
12 NetworkNeuroscience 490
ALBERTOCACCIOLA,ALESSANDROMUSCOLONI,ANDCARLOVITTORIO
CANNISTRACI
13 Cytoscape:AToolforAnalyzingandVisualizingNetworkData 533
JOHNH.MORRIS
14 AnalysisoftheSignaturesofCancerStemCellsinMalignantTumorsUsing
ProteinInteractomesandtheSTRINGDatabase 593
KRESˇIMIRPAVELIC´,MARKOKLOBUCˇAR,DOLORESKUZELJ,NATASˇAPRZˇULJ,
SANDRAKRALJEVIC´ PAVELIC´
Index 621