Gene expression studies using affymetrix microarrays:
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| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Boca Raton ; London ; New York
CRC Press Taylor & Francis Group
[2009]
|
| Series: | Chapman & Hall/CRC mathematical and computational biology series
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | 327 Seiten Illustrationen, Diagramme |
| ISBN: | 9781420065152 |
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| 245 | 1 | 0 | |a Gene expression studies using affymetrix microarrays |c Hinrich Göhlmann, Willem Talloen |
| 264 | 1 | |a Boca Raton ; London ; New York |b CRC Press Taylor & Francis Group |c [2009] | |
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| 650 | 4 | |a Gene Expression | |
| 650 | 4 | |a Gene expression |x Research |x Methodology | |
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Record in the Search Index
| _version_ | 1804140893251305472 |
|---|---|
| adam_text | CHAPMAN & HALL/CRC MATHEMATICAL AND COMPUTATIONAL BIOLOGY SERIES GENE
EXPRESSION STUDIES USING AFFYMETRIX MICROARRAYS HINRICH GOHLMANN WILLEM
TALLOEN CRC PRESS TAYLOR & FRANCIS GROUP BOCA RATON LONDON NEW YORK CRC
PRESS IS AN IMPRINT OF THE TAYLOR & FRANCIS GROUP AN INFORMA BUSINESS A
CHAPMAN & HALL BOOK CONTENTS LIST OF FIGURES LIST OF TABLES LIST OF
BIOBOXES LIST OF STATSBOXES PREFACE ABBREVIATIONS AND TERMS 1 BIOLOGICAL
QUESTION 1 1.1 WHY GENE EXPRESSION? 1 1.1.1 BIOTECHNOLOGICAL
ADVANCEMENTS 1 1.1.2 BIOLOGICAL RELEVANCE 1 1.2 RESEARCH QUESTION 6
1.2.1 CORRELATIONAL VS. EXPERIMENTAL RESEARCH 6 1.3 MAIN TYPES OF
RESEARCH QUESTIONS 8 1.3.1 COMPARING TWO GROUPS 8 1.3.2 COMPARING
MULTIPLE GROUPS 9 1.3.3 COMPARING TREATMENT COMBINATIONS 10 1.3.4
COMPARING MULTIPLE GROUPS WITH A REFERENCE GROUP . . 12 1.3.5
INVESTIGATING WITHIN-SUBJECT CHANGES 13 1.3.6 CLASSIFYING AND PREDICTING
SAMPLES 14 2 AFFYMETRIX MICROARRAYS 17 2.1 PROBES 18 2.2 PROBESETS 22
2.2.1 STANDARD PROBESET DEFINITIONS 22 2.2.2 ALTERNATIVE CDFS 24 2.3
ARRAY TYPES 29 2.3.1 STANDARD EXPRESSION MONITORING ARRAYS 31 2.3.2 EXON
ARRAYS 31 2.3.3 GENE ARRAYS 35 2.3.4 TILING ARRAYS 36 2.3.5 FOCUSED
ARRAYS 37 2.4 STANDARD LAB PROCESSES 38 2.4.1 IN VITRO TRANSCRIPTION
ASSAY 38 2.4.2 WHOLE TRANSCRIPT SENSE TARGET LABELING ASSAY 39 2.5
AFFYMETRIX DATA QUALITY 39 2.5.1 REPRODUCIBILITY 39 2.5.2 ROBUSTNESS 40
2.5.3 SENSITIVITY 40 RUNNING THE EXPERIMENT 41 3.1 BIOLOGICAL EXPERIMENT
41 3.1.1 BIOLOGICAL BACKGROUND 41 3.1.1.1 AIM/HYPOTHESIS 41 3.1.1.2
TECHNOLOGY PLATFORM 41 3.1.1.3 EXPECTED CHANGES IN MRNA LEVELS 43 3.1.2
SAMPLE 44 3.1.2.1 SELECTION OF APPROPRIATE SAMPLE/TISSUE .... 44 3.1.2.2
SAMPLE TYPES 45 3.1.2.3 SAMPLE HETEROGENEITY 50 3.1.2.4 GENDER 53
3.1.2.5 TIME POINT 53 3.1.2.6 DISSECTION ARTIFACTS 54 3.1.2.7 ARTIFACTS
DUE TO ANIMAL HANDLING 55 3.1.2.8 . RNA QUALITY 57 3.1.2.9 RNA QUANTITY
62 3.1.3 PILOT EXPERIMENT 64 3.1.4 MAIN EXPERIMENT 65 3.1.4.1 CONTROL
EXPERIMENT 66 3.1.4.2 TREATMENT 66 3.1.4.3 BLOCKING 67 3.1.4.4
RANDOMIZATION 67 3.1.4.5 STANDARDIZATION 67 3.1.4.6 MATCHED CONTROLS 67
3.1.4.7 SAMPLE SIZE/REPLICATES/COSTS 68 3.1.4.8 BALANCED DESIGN 68
3.1.4.9 CONTROL SAMPLES 69 3.1.4.10 SAMPLE POOLING 69 3.1.4.11
DOCUMENTATION 71 3.1.5 FOLLOW-UP EXPERIMENTS 72 3.2 MICROARRAY
EXPERIMENT 73 3.2.1 EXTERNAL RNA CONTROLS 73 3.2.2 TARGET SYNTHESIS 74
3.2.3 BATCH EFFECT .... . 76 3.2.4 WHOLE GENOME VS. FOCUSED MICROARRAYS
76 DATA ANALYSIS PREPARATION 79 4.1 DATA PREPROCESSING 79 4.1.1 PROBE
INTENSITY 79 4.1.2 LOG2 TRANSFORMATION 81 4.1.3 BACKGROUND CORRECTION 82
4.1.4 NORMALIZATION 83 4.1.5 SUMMARIZATION 89 4.1.5.1 PM AND MM
TECHNIQUES 90 4.1.5.2 PM ONLY TECHNIQUES 93 4.1.6 ALL IN ONE 95 4.1.7
DETECTION CALLS 96 4.1.7.1 MAS 5.0 97 4.1.7.2 DABG 97 4.1.7.3 PANP 97
4.1.8 STANDARDIZATION 98 4.2 QUALITY CONTROL 99 4.2.1 TECHNICAL DATA 99
4.2.2 PSEUDO-IMAGES 99 4.2.3 EVALUATING REPRODUCIBILITY 99 4.2.3.1
MEASURES FOR EVALUATING REPRODUCIBILITY ... 99 4.2.3.2 A MOTIVATING
EXAMPLE 103 4.2.4 BATCH EFFECTS 106 4.2.5 BATCH EFFECT CORRECTION 109
DATA ANALYSIS 113 5.1 WHY DO WE NEED STATISTICS? 113 5.1.1 THE NEED FOR
DATA INTERPRETATION 114 5.1.2 THE NEED FOR A GOOD EXPERIMENTAL DESIGN
115 5.1.3 STATISTICS VS. BIOINFORRNATICS 115 5.2 THE CURSE OF
HIGH-DIMENSIONALITY 117 5.2.1 ANALYSIS REPRODUCIBILITY 117 5.2.2 SEEK
UNTIL YOU FIND 118 5.3 GENE FILTERING 118 5.3.1 FILTERING APPROACHES 120
5.3.1.1 INTENSITY OF THE SIGNAL 120 5.3.1.2 VARIATION BETWEEN SAMPLES
121 5.3.1.3 ABSENT/PRESENT CALLS 121 5.3.1.4 INFORMATIVE/NON-INFORMATIVE
CALLS 122 5.3.2 IMPACT OF FILTERING ON TESTING AND MULTIPLICITY
CORRECTION 123 5.3.3 COMPARISON OF VARIOUS FILTERING APPROACHES 126 5.4
UNSUPERVISED DATA EXPLORATION 131 5.4.1 MOTIVATION 132 5.4.1.1 BATCH
EFFECTS 132 5.4.1.2 TECHNICAL OR BIOLOGICAL OUTLIERS 132 5.4.1.3 QUALITY
CHECK OF PHENOTYPIC DATA 134 5.4.1.4 IDENTIFICATION OF CO-REGULATED
GENES 134 5.4.2 CLUSTERING 134 5.4.2.1 DISTANCE AND LINKAGE 135 5.4.2.2
CLUSTERING ALGORITHMS 139 5.4.2.3 QUALITY CHECK OF CLUSTERING 147 5.4.3
MULTIVARIATE PROJECTION METHODS 148 5.4.3.1 TYPES OF MULTIVARIATE
PROJECTION METHODS . . 148 5.4.3.2 BIPLOT 152 5.5 DETECTING DIFFERENTIAL
EXPRESSION 153 5.5.1 A SIMPLE SOLUTION FOR A COMPLEX QUESTION 153 5.5.2
TEST STATISTIC 155 5.5.2.1 FOLD CHANGE 155 5.5.2.2 TYPES OF T-TESTS 156
5.5.2.3 FROM T-STATISTICS TO P-VALUES 165 5.5.2.4 COMPARISON OF METHODS
168 5.5.2.5 LINEAR MODELS 173 5.5.3 CORRECTION FOR MULTIPLE TESTING 185
5.5.3.1 THE PROBLEM OF MULTIPLE TESTING 185 5.5.3.2 MULTIPLICITY
CORRECTION PROCEDURES 186 5.5.3.3 COMPARISON OF METHODS 192 5.5.3.4
POST-HOC COMPARISONS 194 5.5.4 STATISTICAL SIGNIFICANCE VS. BIOLOGICAL
RELEVANCE 195 5.5.5 SAMPLE SIZE ESTIMATION 196 5.6 SUPERVISED PREDICTION
, . . 197 5.6.1 CLASSIFICATION VS. HYPOTHESIS TESTING 198 5.6.2
CHALLENGES OF MICROARRAY CLASSIFICATION 199 5.6.2.1 OVERFITTING 199
5.6.2.2 THE BIAS-VARIANCE TRADE-OFF 201 5.6.2.3 CROSS-VALIDATION 202
5.6.2.4 NON-UNIQUENESS OF CLASSIFICATION SOLUTIONS . . 203 5.6.3 FEATURE
SELECTION METHODS 204 5.6.4 CLASSIFICATION METHODS 210 5.6.4.1
DISCRIMINANT ANALYSIS 210 5.6.4.2 NEAREST NEIGHBOR CLASSIFIER 210
5.6.4.3 LOGISTIC REGRESSION 211 5.6.4.4 NEURAL NETWORKS 213 5.6.4.5
SUPPORT VECTOR MACHINES 214 5.6.4.6 CLASSIFICATION TREES 215 5.6.4.7
ENSEMBLE METHODS 215 5.6.4.8 PAM 217 5.6.4.9 COMPARISON OF THE METHODS
217 5.6.5 COMPLEX PREDICTION PROBLEMS 218 5.6.5.1 MULTICLASS PROBLEMS
218 5.6.5.2 PREDICTION OF SURVIVAL .* 218 5.6.6 SAMPLE SIZES 218 5.7
PATHWAY ANALYSIS 219 5.7.1 STATISTICAL APPROACHES IN PATHWAY ANALYSIS
220 5.7.1.1 OVER-REPRESENTATION ANALYSIS 220 5.7.1.2 FUNCTIONAL CLASS
SCORING 221 5.7.1.3 GENE SET ANALYSIS 221 5.7.1.4 COMPARISON OF THE
METHODS 223 5.7.2 DATABASES 224 5.7.2.1 GENE ONTOLOGY 228 5.7.2.2 KEGG
228 5.7.2.3 GENMAPP 228 5.7.2.4 ARED 229 5.7.2.5 CMAP 229 5.7.2.6
BIOCARTA 229 5.7.2.7 CHROMOSOMAL LOCATION 229 5.8 OTHER ANALYSIS
APPROACHES 230 5.8.1 GENE NETWORK ANALYSIS 230 5.8.2 META-ANALYSIS 231
5.8.3 CHROMOSOMAL LOCATION 232 PRESENTATION OF RESULTS 235 6.1 DATA
VISUALIZATION 235 6.1.1 HEATMAP . . 235 6.1.2 INTENSITY PLOT 238 6.1.3
GENE LIST PLOT 239 6.1.4 VENN DIAGRAM 242 6.1.5 SCATTER PLOTS 243
6.1.5.1 VOLCANO PLOT 243 6.1.5.2 MA PLOT 244 6.1.5.3 SCATTER PLOTS FOR
HIGH-DIMENSIONAL DATA . . . 246 6.1.6 HISTOGRAM 247 6.1.7 BOX PLOT , 249
6.1.8 VIOLIN PLOT 249 6.1.9 DENSITY PLOT 250 6.1.10 DENDROGRAM 250
6.1.11 PATHWAYS WITH GENE EXPRESSION 252 6.1.12 FIGURES FOR PUBLICATION
254 6.2 BIOLOGICAL INTERPRETATION 255 6.2.1 IMPORTANT DATABASES 255
6.2.1.1 ENTREZ GENE 255 6.2.1.2 NETAFFX 256 6.2.1.3 OMIM 256 6.2.2 TEXT
MINING 256 6.2.3 DATA INTEGRATION 256 6.2.3.1 DATA FROM MULTIPLE
MOLECULAR SCREENINGS . . 256 6.2.3.2 SYSTEMS BIOLOGY 257 6.2.4 RTQPCR
VERIFICATION 257 6.3 DATA PUBLISHING 258 6.3.1 ARRAYEXPRESS 259 6.3.2
GENE EXPRESSION OMNIBUS 259 6.4 REPRODUCIBLE RESEARCH 260 7
PHARMACEUTICAL R&D 261 7.1 THE NEED FOR EARLY INDICATIONS 261 7.2
CRITICAL PATH INITIATIVE 262 7.3 DRUG DISCOVERY 264 7.3.1 DIFFERENCES
BETWEEN NORMAL AND DISEASED TISSUES . . . 264 7.3.2 DISEASE SUBCLASS
DISCOVERY 265 7.3.3 IDENTIFICATION OF MOLECULAR TARGETS 265 7.3.4
PROFILING FOR MOLECULAR CHARACTERIZATION 266 7.3.5 CHARACTERIZATION OF A
DISEASE MODEL 266 7.3.6 COMPOUND PROFILING 268 7.3.7 DOSE-RESPONSE
TREATMENT 269 7.4 DRUG DEVELOPMENT 270 7.4.1 BIOMARKERS 270 7.4.2
RESPONSE SIGNATURES 273 7.4.3 TOXIGENOMICS 274 7.5 CLINICAL TRIALS 276
7.5.1 EFFICACY MARKERS 276 7.5.2 SIGNATURES FOR OUTCOME PROGNOSIS 276 8
USING R AND BIOCONDUCTOR 279 8.1 R AND BIOCONDUCTOR 280 8.2 R AND SWEAVE
281 8.3 R AND ECLIPSE 282 8.4 AUTOMATED ARRAY ANALYSIS 283 8.4.1 LOAD
PACKAGES 283 8.4.2 GENE FILTERING 284 8.4.3 UNSUPERVISED EXPLORATION 284
8.4.4 TESTING FOR DIFFERENTIAL EXPRESSION 284 8.4.5 SUPERVISED
CLASSIFICATION 285 8.5 OTHER SOFTWARE FOR RNICROARRAY ANALYSIS 286 9
FUTURE PERSPECTIVES 289 9.1 CO-ANALYZING DIFFERENT DATA TYPES 289 9.2
THE MICROARRAYS OF THE FUTURE 290 9.3 NEXT-GEN SEQUENCING: THE END FOR
MICROARRAYS? 292 BIBLIOGRAPHY 297 INDEX 321
|
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| illustrated | Illustrated |
| indexdate | 2024-07-09T22:07:13Z |
| institution | BVB |
| isbn | 9781420065152 |
| language | English |
| lccn | 2009009976 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-018766771 |
| oclc_num | 166358453 |
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| owner | DE-19 DE-BY-UBM DE-578 |
| owner_facet | DE-19 DE-BY-UBM DE-578 |
| physical | 327 Seiten Illustrationen, Diagramme |
| publishDate | 2009 |
| publishDateSearch | 2009 |
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| publisher | CRC Press Taylor & Francis Group |
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| series2 | Chapman & Hall/CRC mathematical and computational biology series |
| spelling | Göhlmann, Hinrich Verfasser aut Gene expression studies using affymetrix microarrays Hinrich Göhlmann, Willem Talloen Boca Raton ; London ; New York CRC Press Taylor & Francis Group [2009] © 2009 327 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Chapman & Hall/CRC mathematical and computational biology series Includes bibliographical references and index Oligonucleotide Array Sequence Analysis - methods DNA microarrays Gene Expression Gene expression Research Methodology Microarray Analysis methods Oligonucleotide Array Sequence Analysis methods Talloen, Willem Verfasser aut HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018766771&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Göhlmann, Hinrich Talloen, Willem Gene expression studies using affymetrix microarrays Includes bibliographical references and index Oligonucleotide Array Sequence Analysis - methods DNA microarrays Gene Expression Gene expression Research Methodology Microarray Analysis methods Oligonucleotide Array Sequence Analysis methods |
| title | Gene expression studies using affymetrix microarrays |
| title_auth | Gene expression studies using affymetrix microarrays |
| title_exact_search | Gene expression studies using affymetrix microarrays |
| title_full | Gene expression studies using affymetrix microarrays Hinrich Göhlmann, Willem Talloen |
| title_fullStr | Gene expression studies using affymetrix microarrays Hinrich Göhlmann, Willem Talloen |
| title_full_unstemmed | Gene expression studies using affymetrix microarrays Hinrich Göhlmann, Willem Talloen |
| title_short | Gene expression studies using affymetrix microarrays |
| title_sort | gene expression studies using affymetrix microarrays |
| topic | Oligonucleotide Array Sequence Analysis - methods DNA microarrays Gene Expression Gene expression Research Methodology Microarray Analysis methods Oligonucleotide Array Sequence Analysis methods |
| topic_facet | Oligonucleotide Array Sequence Analysis - methods DNA microarrays Gene Expression Gene expression Research Methodology Microarray Analysis methods Oligonucleotide Array Sequence Analysis methods |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018766771&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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