DNA microarrays and gene expression: from experiments to data analysis and modeling
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| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Cambridge [u.a.]
Cambridge Univ. Press
2002
|
| Edition: | 1. publ. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XVI, 213 S. graph. Darst. |
| ISBN: | 0521800226 |
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Record in the Search Index
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| adam_text | DNA MICROARRAYS AND
GENE EXPRESSION
From experiments to data analysis and modeling
PIERRE BALDI
University of California, Irvine
and
G WESLEY HATFIELD
University of California Irvine
CAMBRIDGE
UNIVERSITY PRESS
Contents
Preface page viii
1 A brief history of genomics 1
2 DNA array formats 7
In situ synthesized oligonucleotide arrays 7
Pre-synthesized DNA arrays 11
Filter-based DNA arrays 12
Non-conventional gene expression profiling technologies 13
3 DNA array readout methods 17
Reading data from a fluorescent signal 17
Reading data from a radioactive signal 21
4 Gene expression profiling experiments: Problems, pitfalls, and
solutions 29
Primary sources of experimental and biological variation 29
Special considerations for gene expression profiling in
bacteria 32
Problems associated with target preparation with
polyadenylated mRNA from eukaryotic cells 42
A total RNA solution for target preparation from eukaryotic
cells 44
Target cDNA synthesis and radioactive labeling for
pre-synthesized DNA arrays 45
Data acquisition for nylon filter experiments 45
Data acquisition for Affymetrix GeneChip™ glass slide
experiments 48
Normalization methods 49
vi Contents
5 Statistical analysis of array data: Inferring changes 53
Problems and common approaches 53
Probabilistic modeling of array data 55
Simulations 65
Extensions 69
6 Statistical analysis of array data: Dimensionality reduction,
clustering, and regulatory regions 73
Problems and approaches 73
Visualization, dimensionality reduction, and principal
component analysis 75
Clustering overview 78
Hierarchical clustering 82
K-means, mixture models, and EM algorithms 85
DNA arrays and regulatory regions 90
7 The design, analysis, and interpretation of gene expression
profiling experiments 97
Experimental design 99
Identification of differentially expressed genes 100
Determination of the source of errors in DNA array
experiments 101
Estimation of the global false positive level for a DNA array
experiment 103
Improved statistical inference from DNA array data using a
Bayesian statistical framework 109
Nylon filter data vs Affymetrix GeneChip™ data 109
Modeling probe pair set data from Affymetrix GeneChips™ 124
Application of clustering and visualization methods 124
Identification of differential gene expression patterns resulting
from two-variable perturbation experiments 125
8 Systems biology 135
Introduction 135
The molecular world: Representation and simulation 137
Computational models of regulatory networks 146
Software and databases 163
The search for general principles 165
Contents vii
Appendix A Experimental protocols 177
Appendix B Mathematical complements 185
Appendix C Internet resources 195
Appendix D CyberT: An online program for the statistical analysis
of DNA array data 199
Index 207
|
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| spelling | Baldi, Pierre Verfasser aut DNA microarrays and gene expression from experiments to data analysis and modeling Pierre Baldi and G. Wesley Hatfield 1. publ. Cambridge [u.a.] Cambridge Univ. Press 2002 XVI, 213 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biologia molecular larpcal DNA Microarrays gtt Dna larpcal Expressão gênica larpcal Genexpressie gtt Statistische modellen gtt DNA microarrays Gene expression Genexpression (DE-588)4020136-3 gnd rswk-swf Microarray (DE-588)4544227-7 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf DNS (DE-588)4070512-2 s Genexpression (DE-588)4020136-3 s Microarray (DE-588)4544227-7 s DE-604 Hatfield, G. Wesley Verfasser aut HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009883655&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Baldi, Pierre Hatfield, G. Wesley DNA microarrays and gene expression from experiments to data analysis and modeling Biologia molecular larpcal DNA Microarrays gtt Dna larpcal Expressão gênica larpcal Genexpressie gtt Statistische modellen gtt DNA microarrays Gene expression Genexpression (DE-588)4020136-3 gnd Microarray (DE-588)4544227-7 gnd DNS (DE-588)4070512-2 gnd |
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| title | DNA microarrays and gene expression from experiments to data analysis and modeling |
| title_auth | DNA microarrays and gene expression from experiments to data analysis and modeling |
| title_exact_search | DNA microarrays and gene expression from experiments to data analysis and modeling |
| title_full | DNA microarrays and gene expression from experiments to data analysis and modeling Pierre Baldi and G. Wesley Hatfield |
| title_fullStr | DNA microarrays and gene expression from experiments to data analysis and modeling Pierre Baldi and G. Wesley Hatfield |
| title_full_unstemmed | DNA microarrays and gene expression from experiments to data analysis and modeling Pierre Baldi and G. Wesley Hatfield |
| title_short | DNA microarrays and gene expression |
| title_sort | dna microarrays and gene expression from experiments to data analysis and modeling |
| title_sub | from experiments to data analysis and modeling |
| topic | Biologia molecular larpcal DNA Microarrays gtt Dna larpcal Expressão gênica larpcal Genexpressie gtt Statistische modellen gtt DNA microarrays Gene expression Genexpression (DE-588)4020136-3 gnd Microarray (DE-588)4544227-7 gnd DNS (DE-588)4070512-2 gnd |
| topic_facet | Biologia molecular DNA Microarrays Dna Expressão gênica Genexpressie Statistische modellen DNA microarrays Gene expression Genexpression Microarray DNS |
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