Statistical Methods in Molecular Biology

Thisbookisrecommendedforuseassupplementarymaterialbothinsideandoutside classroomsorasaself-learningguideforstudentsscientistsandresearcherswhodealwith numericdatainmolecularbiologyandrelated?elds. Thosewhostartasbeginnersbut desiretobeatanintermediatelevelwill?ndthisbookespeciallyusefulintheirlearning pathway. WewanttothankJohnWalker(serieseditor)PatrickMartonDavidCaseyandAnne Meagher(editorsatSpringerandHumana)andShanthyJaganathan(Integra-India). The followingpersonsprovidedusefuladviceandcommentsonselectionoftopicsreferralto expertsineachtopicand/orchapterreviewsthatwetrulyappreciate:StephenLooney(a former editor of this book) Stan Young Dmitri Zaykin Douglas Hawkins Wei Pan Alexandre Almeida John Ho Rebecca Doerge Paula Trushin Kevin Morgan Jason OsbornePeterWestfallJennyXiangYa-linChiuYolandaBarronHuiboShaoAlvin MushlinandRonaldFanta. Drs. BangZhouandMazumdarwerepartiallysupported byClinicalTranslationalScienceCenter(CTSC)grant(UL1-RR024996). HeejungBang vii Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi PARTIBASICSTATISTICS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1. ExperimentalStatisticsforBiologicalSciences. . . . . . . . . . . . . . . . . . . 3 HeejungBangandMarieDavidian 2. NonparametricMethodsforMolecularBiology. . . . . . . . . . . . . . . . . . 105 KnutM. WittkowskiandTingtingSong 3. BasicsofBayesianMethods. . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 SujitK. Ghosh 4. TheBayesiant-TestandBeyond . . . . . . . . . . . . . . . . . . . . . . . . . 179 MithatGönen PARTII DESIGNSANDMETHODSFORMOLECULARBIOLOGY. . . . . . . . . . 201 5. SampleSizeandPowerCalculationforMolecularBiologyStudies. . . . . . . . 203 Sin-HoJung 6. DesignsforLinkageAnalysisandAssociationStudiesofComplexDiseases. . . . 219 YuehuaCuiGengxinLiShaoyuLiandRonglingWu 7. IntroductiontoEpigenomicsandEpigenome-WideAnalysis. . . . . . . . . . . 243 MelissaJ. FazzariandJohnM. Greally 8. ExplorationVisualizationandPreprocessingofHigh–DimensionalData. . . . 267 ZhijinWuandZhiqiangWu PARTIII STATISTICALMETHODSFORMICROARRAYDATA . . . . . . . . . . . . 285 9. IntroductiontotheStatisticalAnalysisofTwo-ColorMicroarrayData. . . . . . 287 MartinaBremerEdwardHimelblauandAndreasMadlung 10. BuildingNetworkswithMicroarrayData. . . . . . . . . . . . . . . . . . . . . 315 BradleyM. BroomWareeRinsurongkawongLajosPusztai andKim-AnhDo PARTIV ADVANCEDORSPECIALIZEDMETHODSFORMOLECULARBIOLOGY. . 345 11. SupportVectorMachinesforClassi?cation:AStatisticalPortrait. . . . . . . . . 347 YoonkyungLee 12. AnOverviewofClusteringAppliedtoMolecularBiology . . . . . . . . . . . . 369 RebeccaNugentandMarinaMeila ix xContents 13. HiddenMarkovModelandItsApplicationsinMotifFindings. . . . . . . . . . 405 JingWuandJunXie 14. DimensionReductionforHigh-DimensionalData. . . . . . . . . . . . . . . . 417 LexinLi 15. IntroductiontotheDevelopmentandValidationofPredictiveBiomarker ModelsfromHigh-ThroughputDataSets . . . . . . . . . . . . . . . . . . . . 435 XutaoDengandFabienCampagne 16. Multi-geneExpression-basedStatisticalApproachestoPredicting Patients’ClinicalOutcomesandResponses. . . . . . . . . . . . . . . . . . . . 471 FengChengSang-HoonChoandJaeK. Lee 17. Two-StageTestingStrategiesforGenome-WideAssociationStudies inFamily-BasedDesigns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 485 AmyMurphyScottT. WeissandChristophLange 18. StatisticalMethodsforProteomics . . . . . . . . . . . . . . . . . . . . . . . . 497 KlausJung PARTVMETA-ANALYSISFORHIGH-DIMENSIONALDATA . . . . . . . . . . . . 509 19. StatisticalMethodsforIntegratingMultipleTypesofHigh-ThroughputData. . 511 YangXieandChulAhn 20. ABayesianHierarchicalModelforHigh-DimensionalMeta-analysis. . . . . . . 531 FeiLiu 21. MethodsforCombiningMultipleGenome-WideLinkageStudies. . . . . . . . 541 TreciaA. Kippolaan