With the completion of the human genome project, followed by the rise in high-throughput technologies like the various microarray and now high throughput genomic sequencing platforms,weexperiencedthebirthofSystemsBiologyafteritslonggestation. Thisrevolutionis markedbyachangeintheresearchparadigmfromthesinglesmall-scaleexperiment,i. e. ,following thechangeofacomponentinamulticomponentsystem,toonethatattemptstosimultaneously monitorthechangeoftensofthousandsofmoleculeswithinthisbody. Thisclearlynecessitatesthe unparalleleduseofproject-specificinformatictools,which,todate,requiresanunprecedentedlevel ofdevelopmenttocollect,manageandminethedataforinterestingassociations. Tobegintounderstandthisinformationwenowrelyonstatisticalanalysistoaidinourselection ofthefruitfromthetree. However,thisoftentakesusonajourneyintoanewfieldforwhichweare notyetprepared. SamuelJohnson(1709-1784)foreshadowedthedilemmawewouldfaceand characterizeditasfollows:"Knowledgeisoftwokinds. Weknowasubjectourselves,orweknow wherewecanfindinformationonit. "Itisforthelatterthatweroutinelyturntotheliterature. The rateofgrowthoftheliteratureparallelsthatofsequencingdataandthearraydataplacingan almostimpossibletaskbeforeeachinvestigator. Topartiallyeasethisburdenweareagainturning towardsdevelopinginformaticaidsthatminetheliteratureanddatatodevelopsummariesand associationstodirectlyaddressthequestionsposedandthenewhypothesesthataretobetested. Althoughmoreclearlyarticulated,weagainfacesimilarchallengesasthosetackledduringthe courseofthehumangenomeproject. Itisessentialthatthetrainingofthebiologistandcomput- scientistoccurinaninterdisciplinaryenvironmentofcross-fertilization. Withthisgoalinmindthe textbook"BioinformaticsforSystemsBiology"wasundertaken. WebeginthisexplorationwithPartI,toprovidethecomputerscientistwithanintroductiontothe underlyingprinciplesofcellbiology. ThisisfollowedbyabriefintroductioninPartIIasameansfor thebiologisttobecomefamiliarwithconceptsandthestatisticalanalysisoflargedatasets. PartIII thendescribes,todate,thebestcharacterizeduseofthemicroarrayplatformthatisnowmoving towardswholegenomeanalysis. Withallofthisdata,howdowebeginanalysisforcommonelements guidingtheunderlyingprinciples?ThisisdiscussedinPartIVwhichleadstoPartVandPartVIto test,insilico,therelationshipsonawidescaleinordertoassesstheirapplicability. Upondeveloping theassociations,PartVIIaskshowdoesthisinformationrelatetowhatwasmeasured?Asthesebasic principlesaredevelopedfroman"omics"drivenbiologicalsystemsapproach,theyareappliedin PartVIIItotranslationalmedicine. Anexcellentexampleisthenewterm"personalizedmedicine" thatisbeginningtoreverberateinclinicalcare. ItistheculminationoftheSystemsBiologyrevolution wheretechnologicaladvancesandcross-fertilizationhavedriventhefieldtomaturetothepoint whereitisbeingincorporatedinatruebench-to-bedsidemanner. Asyoureadthechapters,youwillfindthattheycanstandalone,yetcanbecombinedto emphasizetheintegralroleofinformaticsinSystemsBiology. Mostofthefiguresandtablesarein greyscale. IwouldencourageyoutoviewthosethatbenefitfromcolorontheaccompanyingCD. ThematerialcontainedontheCDprovidesanexcellentsourceofslidesforyourlecturesand presentations. v vi Preface Thechapter-relatedGlossaryandAbbreviationssectionwillassistinfamiliarizingyouwiththe terms. Youwillalsofindtheliteratureandsuggestedreadingsections,includingkeyreferences, veryusefulasyoudelveintothesubjectmatter. Technology,byitsverymeaningimpliesrefinement and change. The informatics approaches used in systems biology are continually subject to refinement. Withthisreality,youareencouragedtoutilizethewebsiteinformationprovidedin variouschapterstohelpaccessthemostcurrentinformationandresourcesavailable. AsSystems Biologydevelopsweareabletowitnessgrowingpainsandmilestones. Withcontinuedinformatic andbiologicalcross-fertilization,advancementsinSystemsBiologywillrevolutionizepersonalized medicineansweringquestionsbyintegratinginformationinunexpectedways. Contents PartI LifeofaCellandItsAnalysis...1 1 StructureandFunctionoftheNucleusandCellOrganelles...3 JonHolyandEdPerkins 2 TranscriptionandtheControlofGeneExpression...33 NadineWiper-BergeronandIlonaS. Skerjanc 3 RNAProcessingandTranslation...51 ChristinaKaramboulas,NadineWiper-Bergeron,andIlonaS. Skerjanc 4 DNAReplication,Recombination,andRepair...67 LindaB. Bloom 5 CellSignaling...89 DanielA. RappoleeandD. RandallArmant 6 EpigeneticsofSpermiogenesis-drivenbiologicalsystemsapproach,theyareappliedin PartVIIItotranslationalmedicine. Anexcellentexampleisthenewterm"personalizedmedicine" thatisbeginningtoreverberateinclinicalcare. ItistheculminationoftheSystemsBiologyrevolution wheretechnologicaladvancesandcross-fertilizationhavedriventhefieldtomaturetothepoint whereitisbeingincorporatedinatruebench-to-bedsidemanner. Asyoureadthechapters,youwillfindthattheycanstandalone,yetcanbecombinedto emphasizetheintegralroleofinformaticsinSystemsBiology. Mostofthefiguresandtablesarein greyscale. IwouldencourageyoutoviewthosethatbenefitfromcolorontheaccompanyingCD. ThematerialcontainedontheCDprovidesanexcellentsourceofslidesforyourlecturesand presentations. v vi Preface Thechapter-relatedGlossaryandAbbreviationssectionwillassistinfamiliarizingyouwiththe terms. Youwillalsofindtheliteratureandsuggestedreadingsections,includingkeyreferences, veryusefulasyoudelveintothesubjectmatter. Technology,byitsverymeaningimpliesrefinement and change. The informatics approaches used in systems biology are continually subject to refinement. Withthisreality,youareencouragedtoutilizethewebsiteinformationprovidedin variouschapterstohelpaccessthemostcurrentinformationandresourcesavailable. AsSystems Biologydevelopsweareabletowitnessgrowingpainsandmilestones. Withcontinuedinformatic andbiologicalcross-fertilization,advancementsinSystemsBiologywillrevolutionizepersonalized medicineansweringquestionsbyintegratinginformationinunexpectedways. Contents PartI LifeofaCellandItsAnalysis...1 1 StructureandFunctionoftheNucleusandCellOrganelles...3 JonHolyandEdPerkins 2 TranscriptionandtheControlofGeneExpression...33 NadineWiper-BergeronandIlonaS. Skerjanc 3 RNAProcessingandTranslation...51 ChristinaKaramboulas,NadineWiper-Bergeron,andIlonaS. Skerjanc 4 DNAReplication,Recombination,andRepair...67 LindaB. Bloom 5 CellSignaling...89 DanielA. RappoleeandD. RandallArmant 6 EpigeneticsofSpermiogenesis-CombiningInSilicoandProteomicApproaches intheMouseModel...105 SophieRousseauxandMyriamFerro 7 GenomicToolsforAnalyzingTranscriptionalRegulatoryNetworks...119 JohnJ. Wyrick PartII StatisticalToolsandTheirApplication...137 8 ProbabilityandHypothesisTesting...139 MichaelL. Kruger 9 StochasticModelsforBiologicalPatterns...151 GautamB. Singh 10 PopulationGenetics...163 JillS. Barnholtz-SloanandHemantK. Tiwari 11 StatisticalToolsforGeneExpressionAnalysisandSystemsBiology andRelatedWebResources...1 81 ChiaraRomualdiandGerolamoLanfranchi vii viii Contents PartIII TranscriptomeAnalysis...207 12 WhatGoesinisWhatComesOut:HowtoDesignandImplementaSuccessful MicroarrayExperiment...209 JeffreyA. LoebandThomasL. Beaumont 13 ToolsandApproachesforanEnd-to-EndExpressionArrayAnalysis...227 AdrianE. PlattsandStephenA. Krawetz 14 AnalysisofAlternativeSplicingwithMicroarrays...267 JingyiHui,ShivendraKishore,AmitKhanna,andStefanStamm PartIV StructuralandFunctionalSequenceAnalysis...281 15 AnIntroductiontoMultipleSequenceAlignment-andtheT-CoffeeShop. BeyondJust AligningSequences:HowGoodcanyouMakeyourAlignment,andsoWhat?...283 StevenM. Thompson 16 ASpectrumofPhylogenetic-BasedApproachesforPredictingProtein FunctionalSites...315 DukkaBahadurK. C. andDennisR. Livesay 17 TheRoleofTranscriptionFactorBindingSitesinPromotersandTheir InSilicoDetection...339 ThomasWerner 18 InSilicoDiscoveryofDNARegulatorySitesandModules...353 PanayiotisV. Benos PartV LiteratureMiningforAssociationandMeaning...367 19 MiningtheResearchLiteratureinSystemsBiology...369 KeirT. Reavie 20 GoPubMed:ExploringPubMedwithOntologicalBackgroundKnowledge...385 HeikoDietze,DimitraAlexopoulou,MichaelR.

Life of a Cell and its Analysis: Structure and Function of the Nucleus and Cell Organelles.- Transcription and the Control of Gene Expression.- RNA Processing and Translation.- DNA Replication, Recombination, and Repair.- Cell signalling.- Epigenetics of Spermiogenesis: combining in silico and proteomic approaches in the mouse model.- Genomic Tools for Analyzing Transcriptional Regulatory Networks.- Statistical Tools and Their Application: Probability and Hypothesis Testing.- Stochastic Models for Biological Patterns.- Population Genetics.- Statistical tools for gene expression analysis and system biology and related web resources.- Transcriptome Analysis: What goes in is what comes out: How to design and implement a successful microarray experiment.- Tools and Approaches for an End-to-End Expression Array Analysis.- Analysis of alternative splicing with microarrays.- Structural and Functional Sequence Analysis: An Introduction to Multiple Sequence Alignment - and the T-Coffee Shop. Beyond just aligning sequences: how good can you make your alignment, and so what?.- A spectrum of phylogenetic-based approaches for predicting protein functional sites.- The role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection.- In silico Discovery of DNA Regulatory Sites and Modules.-Literature Mining for Association and Meaning: Mining the Research Literature in Systems Biology.- GoPubMed: Exploring PubMed with Ontological Background Knowledge.- BiblioSphere - Hypothesis Generation in Regulatory Network Analysis.- Biological Knowledge Extraction.- Genomic Databases: Using KEGG in the Transition from Genomics to Chemical Genomics.- Ensembl: Open-Source Software for Large-Scale Genome Analysis.- Management of spatially organised biological data using EMAGE.- Equality of the sexes? Parent-of-origin effects on transcription and de novo mutations.- Biological Networks: Methods for Structural Inference and Functional Module Identification inIntracellular Networks.- Methods for Dynamical Inference in Intracellular Networks.- ASIAN: Network Inference Web Server.- Bridging the Gap: Bioinformatics for Metabolomics.- Virtual Reality Meets Functional Genomics.- Systems Biology of Personalized Medicine.