Bayesian analysis of gene expression data:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Chichester, U.K.
Wiley
2009
|
| Edition: | 1. publ. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Includes bibliographical references and index |
| Physical Description: | XII, 240 S. Ill., graph. Darst. |
| ISBN: | 9780470517666 |
Staff View
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| 245 | 1 | 0 | |a Bayesian analysis of gene expression data |c Bani K. Mallick, David Lee Gold, and Veerabhadran Baladandayuthapani |
| 250 | |a 1. publ. | ||
| 264 | 1 | |a Chichester, U.K. |b Wiley |c 2009 | |
| 300 | |a XII, 240 S. |b Ill., graph. Darst. | ||
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| 500 | |a Includes bibliographical references and index | ||
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| 650 | 7 | |a Bioinformática |2 larpcal | |
| 650 | 7 | |a Estatística aplicada |2 larpcal | |
| 650 | 7 | |a Genética estatística |2 larpcal | |
| 650 | 7 | |a Inferência bayesiana (inferência estatística) |2 larpcal | |
| 650 | 7 | |a Medicina (aplicações) |2 larpcal | |
| 650 | 4 | |a Gene expression |x Statistical methods | |
| 650 | 4 | |a Bayesian statistical decision theory | |
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| 700 | 1 | |a Gold, David |e Sonstige |4 oth | |
| 700 | 1 | |a Baladandayuthapani, Veerabhadran |e Sonstige |4 oth | |
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Record in the Search Index
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| adam_text | BAYESIAN ANALYSIS OF GENE EXPRESSION DATA BANI K. MALLICK, TEXAS A&M
UNIVERSITY, USA DAVID LEE GOLD, UNIVERSITY AT BUFFALO, THE STATE
UNIVERSITY OF NEW YORK, USA AND VEERABHADRAN BALADANDAYUTHAPANI,
UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER, USA ) WILEY A JOHN WILEY
AND SONS, LTD., PUBLICATION CONTENTS TABLE OF NOTATION XI 1
BIOINFORMATICS AND GENE EXPRESSION EXPERIMENTS 1 1.1 INTRODUCTION 1 1.2
ABOUT THIS BOOK 3 2 GENE EXPRESSION DATA: BASIC BIOLOGY AND EXPERIMENTS
5 2.1 BACKGROUND BIOLOGY 5 2.1.1 DNA STRUCTURES AND TRANSCRIPTION 6 2.2
GENE EXPRESSION MICROARRAY EXPERIMENTS 9 2.2.1 MICROARRAY DESIGNS 11
2.2.2 WORK FLOW 11 2.2.3 DATA CLEANING 15 3 BAYESIAN LINEAR MODELS FOR
GENE EXPRESSION * 21 3.1 INTRODUCTION 21 3.2 BAYESIAN ANALYSIS OF A
LINEAR MODEL 22 3.2.1 ANALYSIS VIA CONJUGATE PRIORS 23 3.2.2 BAYESIAN
VARIABLE SELECTION 25 3.2.3 MODEL SELECTION PRIORS 26 3.2.4 PRIORS ON
REGRESSION COEFFICIENTS 27 3.2.5 SPARSITY PRIORS 29 3.3 BAYESIAN LINEAR
MODELS FOR DIFFERENTIAL EXPRESSION 30 3.3.1 RELEVANT WORK 32 3.4
BAYESIAN ANOVA FOR GENE SELECTION 34 3.4.1 THE BASIC BAYESIAN ANOVA
MODEL 35 3.4.2 DIFFERENTIAL EXPRESSION VIA MODEL SELECTION 36 3.5 ROBUST
ANOVA MODEL WITH MIXTURES OF SINGULAR DISTRIBUTIONS 38 3.6 CASE STUDY 40
3.7 ACCOUNTING FOR NUISANCE EFFECTS 43 3.8 SUMMARY AND FURTHER READING
49 4 BAYESIAN MULTIPLE TESTING AND FALSE DISCOVERY RATE ANALYSIS 51 4.1
INTRODUCTION TO MULTIPLE TESTING 51 VIII CONTENTS 4.2 FALSE DISCOVERY
RATE ANALYSIS 53 4.2.1 THEORETICAL DEVELOPMENTS 53 4.2.2 FDR ANALYSIS
WITH GENE EXPRESSION ARRAYS 57 4.3 BAYESIAN FALSE DISCOVERY RATE
ANALYSIS 60 4.3.1 THEORETICAL DEVELOPMENTS 60 4.4 BAYESIAN ESTIMATION OF
FDR 61 4.5 FDR AND DECISION THEORY 65 4.6 FDR AND BFDR SUMMARY 65 5
BAYESIAN CLASSIFICATION FOR MICROARRAY DATA 69 5.1 INTRODUCTION 69 5.2
CLASSIFICATION AND DISCRIMINANT RULES 71 5.3 BAYESIAN DISCRIMINANT
ANALYSIS 72 5.4 BAYESIAN REGRESSION BASED APPROACHES TO CLASSIFICATION
74 5.4.1 BAYESIAN ANALYSIS OF GENERALIZED LINEAR MODELS 75 5.4.2 LINK
FUNCTIONS 75 5.4.3 GLM USING LATENT PROCESSES 76 5.4.4 PRIORS AND
COMPUTATION 76 5.4.5 BAYESIAN PROBIT REGRESSION USING AUXILIARY
VARIABLES 77 5.5 BAYESIAN NONLINEAR CLASSIFICATION 79 5.5.1
CLASSIFICATION USING INTERACTIONS 79 5.5.2 CLASSIFICATION USING KERNEL
METHODS 82 5.6 PREDICTION AND MODEL CHOICE 84 5.7 EXAMPLES 85 5.8
DISCUSSION 87 6 BAYESIAN HYPOTHESIS INFERENCE FOR GENE CLASSES 89 6.1
INTERPRETING MICROARRAY RESULTS 89 6.2 GENE CLASSES 90 6.2.1 ENRICHMENT
ANALYSIS 92 6.3 BAYESIAN ENRICHMENT ANALYSIS 94 6.4 MULTIVARIATE GENE
CLASS DETECTION 95 6.4.1 EXTENDING THE BAYESIAN ANOVA MODEL 98 6.4.2
BAYESIAN DECOMPOSITION 105 6.5 SUMMARY 107 7 UNSUPERVISED CLASSIFICATION
AND BAYESIAN CLUSTERING 109 7.1 INTRODUCTION TO BAYESIAN CLUSTERING FOR
GENE EXPRESSION DATA 109 7.2 HIERARCHICAL CLUSTERING 111 7.3 K -MEANS
CLUSTERING 112 7.4 MODEL-BASED CLUSTERING 114 7.5 MODEL-BASED
AGGLOMERATIVE HIERARCHICAL CLUSTERING 115 7.6 BAYESIAN CLUSTERING 116
7.7 PRINCIPAL COMPONENTS 117 7.8 MIXTURE MODELING 119 CONTENTS IX 7.8.1
LABEL SWITCHING 124 7.9 CLUSTERING USING DIRICHLET PROCESS PRIOR 126
7.9.1 INFINITE MIXTURE OF GAUSSIAN DISTRIBUTIONS 131 8 BAYESIAN
GRAPHICAL MODELS 137 8.1 INTRODUCTION 137 8.2 PROBABILISTIC GRAPHICAL
MODELS . 138 8.3 BAYESIAN NETWORKS 138 8.4 INFERENCE FOR NETWORK MODELS
141 8.4.1 MULTINOMIAL-DIRICHLET MODEL 143 8.4.2 GAUSSIAN MODEL 145 8.4.3
MODEL SEARCH 146 8.4.4 EXAMPLE 148 9 ADVANCED TOPICS 151 9.1
INTRODUCTION 151 9.2 ANALYSIS OF TIME COURSE GENE EXPRESSION DATA 151
9.2.1 GENE SELECTION 152 9.2.2 FUNCTIONAL CLUSTERING 153 9.2.3 DYNAMIC
BAYESIAN NETWORKS 155 9.3 SURVIVAL PREDICTION USING GENE EXPRESSION DATA
155 9.3.1 GENE SELECTION FOR TIME-TO-EVENT OUTCOMES 156 9.3.2 WEIBULL
REGRESSION MODEL 156 9.3.3 PROPORTIONAL HAZARDS MODEL 157 9.3.4
ACCELERATED FAILURE TIME MODEL . 158 APPENDIX A: BASICS OF BAYESIAN
MODELING 159 A.I BASICS 159 A. 1.1 THE GENERAL REPRESENTATION THEOREM
160 A.I.2 BAYES THEOREM 161 A. 1.3 MODELS BASED ON PARTIAL
EXCHANGEABILITY 162 A. 1.4 MODELING WITH PREDICTORS 162 A. 1.5 PRIOR
DISTRIBUTIONS 163 A. 1.6 DECISION THEORY AND POSTERIOR AND PREDICTIVE
INFERENCES 165 A. 1.7 PREDICTIVE DISTRIBUTIONS 168 A. 1.8 EXAMPLES 168
A.2 BAYESIAN MODEL CHOICE 172 A.3 HIERARCHICAL MODELING 175 A.4 BAYESIAN
MIXTURE MODELING 181 A.5 BAYESIAN MODEL AVERAGING 183 APPENDIX B:
BAYESIAN COMPUTATION TOOLS 185 B.I OVERVIEW 185 B.2 LARGE-SAMPLE
POSTERIOR APPROXIMATIONS 186 B.2.1 THE BAYESIAN CENTRAL LIMIT THEOREM
186 X CONTENTS B.2.2 LAPLACE S METHOD 188 B.3 MONTE CARLO INTEGRATION
191 B.4 IMPORTANCE SAMPLING 192 B.5 REJECTION SAMPLING 193 B.6 GIBBS
SAMPLING 195 B.7 THE METROPOLIS ALGORITHM AND METROPOLIS-HASTINGS 198
B.8 ADVANCED COMPUTATIONAL METHODS 202 B.8.1 BLOCK MCMC 203 B.8.2
TRUNCATED POSTERIOR SPACES 204 B.8.3 LATENT VARIABLES AND THE
AUTO-PROBIT MODEL 204 B.8.4 BAYESIAN SIMULTANEOUS CREDIBLE ENVELOPES 205
B.8.5 PROPOSAL UPDATING 206 B.9 POSTERIOR CONVERGENCE DIAGNOSTICS 207
B.10 MCMC CONVERGENCE AND THE PROPOSAL 208 B.I0.1 GRAPHICAL CHECKS FOR
MCMC METHODS 211 B.10.2 CONVERGENCE STATISTICS 212 B.10.3 MCMC IN
HIGH-THROUGHPUT ANALYSIS 213 B.LL SUMMARY 214 REFERENCES 217 INDEX 237
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| spelling | Bayesian analysis of gene expression data Bani K. Mallick, David Lee Gold, and Veerabhadran Baladandayuthapani 1. publ. Chichester, U.K. Wiley 2009 XII, 240 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Biociências larpcal Bioinformática larpcal Estatística aplicada larpcal Genética estatística larpcal Inferência bayesiana (inferência estatística) larpcal Medicina (aplicações) larpcal Gene expression Statistical methods Bayesian statistical decision theory Bayes-Verfahren (DE-588)4204326-8 gnd rswk-swf Statistik (DE-588)4056995-0 gnd rswk-swf Genexpression (DE-588)4020136-3 gnd rswk-swf Bayes-Verfahren (DE-588)4204326-8 s Genexpression (DE-588)4020136-3 s Statistik (DE-588)4056995-0 s DE-604 Mallick, Bani K. 1965- Sonstige (DE-588)124685129 oth Gold, David Sonstige oth Baladandayuthapani, Veerabhadran Sonstige oth HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017997136&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Bayesian analysis of gene expression data Biociências larpcal Bioinformática larpcal Estatística aplicada larpcal Genética estatística larpcal Inferência bayesiana (inferência estatística) larpcal Medicina (aplicações) larpcal Gene expression Statistical methods Bayesian statistical decision theory Bayes-Verfahren (DE-588)4204326-8 gnd Statistik (DE-588)4056995-0 gnd Genexpression (DE-588)4020136-3 gnd |
| subject_GND | (DE-588)4204326-8 (DE-588)4056995-0 (DE-588)4020136-3 |
| title | Bayesian analysis of gene expression data |
| title_auth | Bayesian analysis of gene expression data |
| title_exact_search | Bayesian analysis of gene expression data |
| title_full | Bayesian analysis of gene expression data Bani K. Mallick, David Lee Gold, and Veerabhadran Baladandayuthapani |
| title_fullStr | Bayesian analysis of gene expression data Bani K. Mallick, David Lee Gold, and Veerabhadran Baladandayuthapani |
| title_full_unstemmed | Bayesian analysis of gene expression data Bani K. Mallick, David Lee Gold, and Veerabhadran Baladandayuthapani |
| title_short | Bayesian analysis of gene expression data |
| title_sort | bayesian analysis of gene expression data |
| topic | Biociências larpcal Bioinformática larpcal Estatística aplicada larpcal Genética estatística larpcal Inferência bayesiana (inferência estatística) larpcal Medicina (aplicações) larpcal Gene expression Statistical methods Bayesian statistical decision theory Bayes-Verfahren (DE-588)4204326-8 gnd Statistik (DE-588)4056995-0 gnd Genexpression (DE-588)4020136-3 gnd |
| topic_facet | Biociências Bioinformática Estatística aplicada Genética estatística Inferência bayesiana (inferência estatística) Medicina (aplicações) Gene expression Statistical methods Bayesian statistical decision theory Bayes-Verfahren Statistik Genexpression |
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