A biologist's guide to analysis of DNA microarray data:
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
New York
Wiley-Liss
2002
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XIII, 125, [8] S. Ill. |
| ISBN: | 0471224901 |
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Record in the Search Index
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| adam_text | A BIOLOGIST S GUIDE TO ANALYSIS OF DNA MICROARRAY DATA / KNUDSEN, STEEN : C2002
TABLE OF CONTENTS / INHALTSVERZEICHNIS
PREFACE XI
ACKNOWLEDGMENTS XIII
1 INTRODUCTION I
1.1 HYBRIDIZATION 1
1.2 AFFYMETRIX GENECHIP TECHNOLOGY 3
1.3 SPOTTED ARRAYS 6
1.4 SERIAL ANALYSIS OF GENE EXPRESSION (SAGE) 8
1.5 EXAMPLE: AFFYMETRIX VS. SPOTTED ARRAYS 9
1.6 SUMMARY 11
1.7 FURTHER READING 13
2 OVERVIEW OF DATA ANALYSIS 15
3 BASIC DATA ANALYSIS 17
3.1 ABSOLUTE MEASUREMENTS 17
3.2 SCALING 18
3.2.1 EXAMPLE: LINEAR AND NONLINEAR SCALING 20
3.3 DETECTION OF OUTLIERS 20
3.4 FOLD CHANGE 21
3.5 SIGNIFICANCE 22
3.5.1 NONPARAMETRIC TESTS 24
3.5.2 CORRECTION FOR MULTIPLE TESTING 24
3.5.3 EXAMPLE I: T-TEST AND ANOVA 25
3.5.4 EXAMPLE II: NUMBER OF REPLICATES 26
3.6 SUMMARY 28
3.7 FURTHER READING 29
4 VISUALIZATION BY REDUCTION OF DIMENSIONALITY 33
4.1 PRINCIPAL COMPONENT ANALYSIS 33
4.2 EXAMPLE 1: PCA ON SMALL DATA MATRIX 35
4.3 EXAMPLE 2: PCA ON REAL DATA 37
4.4 SUMMARY 37
4.5 FURTHER READING 39
5 CLUSTER ANALYSIS 41
5.1 HIERARCHICAL CLUSTERING 41
5.2 K-MEANS CLUSTERING 43
5.3 SELF-ORGANIZING MAPS 44
5.4 DISTANCE MEASURES 45
5.4.1 EXAMPLE: COMPARISON OF DISTANCE MEASURES 47
5.5 NORMALIZATION 49
5.6 VISUALIZATION OF CLUSTERS 50
5.6.1 EXAMPLE: VISUALIZATION OF GENE CLUSTERS IN
BLADDER CANCER 50
5.7 SUMMARY 50
5.8 FURTHER READING 52
6 BEYOND CLUSTER ANALYSIS 556.1 FUNCTION PREDICTION 55
6.2 DISCOVERY OF REGULATORY ELEMENTS IN PROMOTER
REGIONS 56
6.2.1 EXAMPLE 1: DISCOVERY OF PROTEASOMAL ELEMENT 57
6.2.2 EXAMPLE 2: REDISCOVERY OF MLU CELL CYCLE
BOX (MCB) 57
6.3 INTEGRATION OF DATA 58
6.4 SUMMARY 59
6.5 FURTHER READING 59
7 REVERSE ENGINEERING OF REGULATORY NETWORKS 63
7.1 THE TIME-SERIES APPROACH 63
7.2 THE STEADY-STATE APPROACH 64
7.3 LIMITATIONS OF NETWORK MODELING 65
7.4 EXAMPLE 1: STEADY-STATE MODEL 65
7.5 EXAMPLE 2: STEADY-STATE MODEL ON REAL DATA 66
7.6 EXAMPLE 3: STEADY-STATE MODEL ON REAL DATA 68
7.7 EXAMPLE 4: LINEAR TIME-SERIES MODEL 68
7.8 FURTHER READING 71
8 MOLECULAR CLASSIFIERS 75
8.1 CLASSIFICATION SCHEMES 76
8.1.1 NEAREST NEIGHBOR 76
8.1.2 NEURAL NETWORKS 76
8.1.3 SUPPORT VECTOR MACHINE 76
8.2 EXAMPLE I: CLASSIFICATION OF CANCER SUBTYPES 77
8.3 EXAMPLE II: CLASSIFICATION OF CANCER SUBTYPES 78
8.4 SUMMARY 79
8.5 FURTHER READING 79
9 SELECTION OF GENES FOR SPOTTING ON ARRAYS 81
9.1 GENE FINDING 82
9.2 SELECTION OF REGIONS WITHIN GENES 82
9.3 SELECTION OF PRIMERS FOR PCR 83
9.4 SELECTION OF UNIQUE OLIGOMER PROBES 83
9.4.1 EXAMPLE: FINDING PCR PRIMERS FOR GENE
AF105374 83
9.5 EXPERIMENTAL DESIGN 84
9.6 FURTHER READING 84
10 LIMITATIONS OF EXPRESSION ANALYSIS 87
10.1 RELATIVE VERSUSABSOLUTERNA QUANTIFICATION 88
10.2 FURTHER READING 88
11 GENOTYPING CHIPS 91
11.1 EXAMPLE: NEURALNETWORKSFOR GENECHIPPREDICTION 91
11.2 FURTHER READING 93
12 SOFTWARE ISSUES AND DATA FORMATS 95
12.1 STANDARDIZATION EFFORTS 96
12.2 STANDARD FILE FORMAT 97
12.2.1 EXAMPLE: SMALL SCRIPTS IN AWK 97
12.3 SOFTWARE FOR CLUSTERING 98
12.3.1 EXAMPLE: CLUSTERING WITH CLUSTARRAY 99
12.4 SOFTWARE FOR STATISTICAL ANALYSIS 99
12.4.1 EXAMPLE: STATISTICALANALYSIS WITH R 9912.4.2 THE AFFYR SOFTWARE PACKAGE 103
12.4.3 COMMERCIAL STATISTICS PACKAGES 103
12.5 SUMMARY 103
12.6 FURTHER READING 104
13 COMMERCIAL SOFTWARE PACKAGES 105
14 BIBLIOGRAPHY 109
INDEX 123.
DIESES SCHRIFTSTUECK WURDE MASCHINELL ERZEUGT.
|
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| language | English |
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| spelling | Knudsen, Steen Verfasser aut A biologist's guide to analysis of DNA microarray data Steen Knudsen Analysis of DNA microarray data New York Wiley-Liss 2002 XIII, 125, [8] S. Ill. txt rdacontent n rdamedia nc rdacarrier Puces à ADN DNA microarrays Oligonucleotide Array Sequence Analysis DNS (DE-588)4070512-2 gnd rswk-swf Datenanalyse (DE-588)4123037-1 gnd rswk-swf Microarray (DE-588)4544227-7 gnd rswk-swf DNS (DE-588)4070512-2 s Microarray (DE-588)4544227-7 s Datenanalyse (DE-588)4123037-1 s DE-604 LoC Fremddatenuebernahme application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009887098&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Knudsen, Steen A biologist's guide to analysis of DNA microarray data Puces à ADN DNA microarrays Oligonucleotide Array Sequence Analysis DNS (DE-588)4070512-2 gnd Datenanalyse (DE-588)4123037-1 gnd Microarray (DE-588)4544227-7 gnd |
| subject_GND | (DE-588)4070512-2 (DE-588)4123037-1 (DE-588)4544227-7 |
| title | A biologist's guide to analysis of DNA microarray data |
| title_alt | Analysis of DNA microarray data |
| title_auth | A biologist's guide to analysis of DNA microarray data |
| title_exact_search | A biologist's guide to analysis of DNA microarray data |
| title_full | A biologist's guide to analysis of DNA microarray data Steen Knudsen |
| title_fullStr | A biologist's guide to analysis of DNA microarray data Steen Knudsen |
| title_full_unstemmed | A biologist's guide to analysis of DNA microarray data Steen Knudsen |
| title_short | A biologist's guide to analysis of DNA microarray data |
| title_sort | a biologist s guide to analysis of dna microarray data |
| topic | Puces à ADN DNA microarrays Oligonucleotide Array Sequence Analysis DNS (DE-588)4070512-2 gnd Datenanalyse (DE-588)4123037-1 gnd Microarray (DE-588)4544227-7 gnd |
| topic_facet | Puces à ADN DNA microarrays Oligonucleotide Array Sequence Analysis DNS Datenanalyse Microarray |
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