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INTEGRATIVE CLUSTER ANALYSIS IN BIOINFORMATICS INTEGRATIVE CLUSTER ANALYSIS IN BIOINFORMATICS Basel Abu-Jamous, Rui Fa and Asoke K. Nandi Brunel University London, UK Thiseditionfirstpublished2015 ©2015JohnWiley&Sons,Ltd RegisteredOffice JohnWiley&Sons,Ltd,TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,UnitedKingdom Fordetailsofourglobaleditorialoffices,forcustomerservicesandforinformationabouthowtoapply forpermissiontoreusethecopyrightmaterialinthisbookpleaseseeourwebsiteatwww.wiley.com. Therightoftheauthortobeidentifiedastheauthorofthisworkhasbeenassertedinaccordancewiththe Copyright,DesignsandPatentsAct1988. Allrightsreserved.Nopartofthispublicationmaybereproduced,storedinaretrievalsystem,ortransmitted, inanyformorbyanymeans,electronic,mechanical,photocopying,recordingorotherwise,exceptaspermitted bytheUKCopyright,DesignsandPatentsAct1988,withoutthepriorpermissionofthepublisher. Wileyalsopublishesitsbooksinavarietyofelectronicformats.Somecontentthatappearsinprintmaynot beavailableinelectronicbooks. Designationsusedbycompaniestodistinguishtheirproductsareoftenclaimedastrademarks.Allbrandnames andproductnamesusedinthisbookaretradenames,servicemarks,trademarksorregisteredtrademarksoftheir respectiveowners.Thepublisherisnotassociatedwithanyproductorvendormentionedinthisbook. LimitofLiability/DisclaimerofWarranty:Whilethepublisherandauthorhaveusedtheirbesteffortsinpreparing thisbook,theymakenorepresentationsorwarrantieswithrespecttotheaccuracyorcompletenessofthecontents ofthisbookandspecificallydisclaimanyimpliedwarrantiesofmerchantabilityorfitnessforaparticularpurpose. Itissoldontheunderstandingthatthepublisherisnotengagedinrenderingprofessionalservicesandneitherthe publishernortheauthorshallbeliablefordamagesarisingherefrom.Ifprofessionaladviceorotherexpert assistanceisrequired,theservicesofacompetentprofessionalshouldbesought. Theadviceandstrategiescontainedhereinmaynotbesuitableforeverysituation.Inviewofongoingresearch, equipmentmodifications,changesingovernmentalregulations,andtheconstantflowofinformationrelatingto theuseofexperimentalreagents,equipment,anddevices,thereaderisurgedtoreviewandevaluatethe informationprovidedinthepackageinsertorinstructionsforeachchemical,pieceofequipment,reagent,or devicefor,amongotherthings,anychangesintheinstructionsorindicationofusageandforaddedwarnings andprecautions.ThefactthatanorganizationorWebsiteisreferredtointhisworkasacitationand/orapotential sourceoffurtherinformationdoesnotmeanthattheauthororthepublisherendorsestheinformationthe organizationorWebsitemayprovideorrecommendationsitmaymake.Further,readersshouldbeawarethat InternetWebsiteslistedinthisworkmayhavechangedordisappearedbetweenwhenthisworkwaswrittenand whenitisread.Nowarrantymaybecreatedorextendedbyanypromotionalstatementsforthiswork.Neitherthe publishernortheauthorshallbeliableforanydamagesarisingherefrom. LibraryofCongressCataloging-in-PublicationData Abu-Jamous,Basel. Integrativeclusteranalysisinbioinformatics/BaselAbu-Jamous,DrRuiFa,andProf.AsokeK.Nandi. pages cm Includesbibliographicalreferencesandindex. ISBN978-1-118-90653-8(cloth) 1. Bioinformatics–Mathematics. 2. Clusteranalysis. I. Fa,Rui. II. Nandi,AsokeKumar. III. Title. QH324.2.A242015 519.53–dc23 2014032428 AcataloguerecordforthisbookisavailablefromtheBritishLibrary. Setin10/12ptTimesbySPiPublisherServices,Pondicherry,India 1 2015 To Wael Abu Jamous and Eman Arafat Hui Jin, Yvonne and Molly Fa Marion, Robin, David and Anita Nandi Brief Contents Preface xix List of Symbols xxi About theAuthors xxiii Part One Introduction 1 1 Introduction to Bioinformatics 3 2 Computational Methods in Bioinformatics 9 Part Two Introduction to Molecular Biology 19 3 The Living Cell 21 4 Central Dogma of Molecular Biology 33 Part Three Data Acquisition and Pre-processing 53 5 High-throughputTechnologies 55 6 Databases, Standards and Annotation 67 7 Normalisation 87 8 Feature Selection 109 9 Differential Expression 119 Part Four ClusteringMethods 133 10 Clustering Forms 135 11 Partitional Clustering 143 12 Hierarchical Clustering 157 13 Fuzzy Clustering 167 14 Neural Network-based Clustering 181 viii BriefContents 15 Mixture Model Clustering 197 16 Graph Clustering 227 17 Consensus Clustering 247 18 Biclustering 265 19 Clustering Methods Discussion 283 Part Five Validation and Visualisation 303 20 Numerical Validation 305 21 Biological Validation 323 22 Visualisations and Presentations 339 Part Six New Clustering Frameworks Designed for Bioinformatics 363 23 Splitting-Merging Awareness Tactics (SMART) 365 24 Tightness-tunable Clustering (UNCLES) 385 Appendix 395 Index 409