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Nederlands Buitenlands   Alles  Titel  Auteur  ISBN        
Levende natuur
Biologie algemeen
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Atul J. Butte Isaac S. Kohane Alvin Kho

Microarrays for an Integrative Genomics

€ 9.95



Taal / Language : English

Inhoudsopgave:
Foreword xi
Preface xiii
Acknowledgments xvii
Introduction
1(36)
The Future Is So Bright...
1(3)
Functional Genomics
4(9)
Informatics and advances in enabling technology
5(5)
Why do we need new techniques?
10(3)
Missing the Forest for the Dendrograms
13(6)
Sociology of a functional genomics pipeline
18(1)
Functional Genomics, Not Genetics
19(6)
In silico analysis will never substitute for in vitro and in vivo
20(5)
Basic Biology
25(12)
Biological caveats in mRNA measurements
31(2)
Sequence-level genomics
33(1)
Proteomics
34(3)
Experimental Design
37(32)
The Safe Conception of a Functional Genomic Experiment
37(23)
Experiment design space
37(2)
Expression space
39(4)
Exercising the expression space
43(10)
Discarding data and low-hanging fruit
53(7)
Gene-Clustering Dogma
60(9)
Supervised versus unsupervised learning
61(2)
Figure of merit: The elusive gold standard in functional genomics
63(6)
Microarray Measurements to Analyses
69(80)
Generic Features of Microarray Technologies
69(19)
Robotically spotted microarrays
73(4)
Oligonuclcotide microarrays
77(11)
Replicate Experiments, Reproducibility, and Noise
88(28)
What is a replicate experiment? A reproducible experimental outcome?
90(2)
Reproducibility across repeated microarray experiments: Absolute expression level and fold difference
92(4)
Cross-platform (technology) reproducibility
96(2)
Pooling sample probes and PCR for replicate experiments
98(1)
What is noise?
99(1)
Sources and examples of noise in the generic microarray experiment
100(9)
Biological variation as noise: The Human Genome Project and irreproducibility of expression measurements
109(3)
Managing noise
112(4)
Prototypical Objectives and Questions
116(5)
Two examples: Inter-array and intra-array
118(3)
Preprocessing: Filters and Normalization
121(6)
Normalization
122(5)
Background on Fold
127(10)
Fold calculation and significance
130(4)
Fold change may not mean the same thing in different expression measurement technologies
134(3)
Dissimilarity and Similarity Measures
137(12)
Linear correlation
139(1)
Entropy and mutual information
140(6)
Dynamics
146(3)
Genomic Data-Mining Techniques
149(66)
Introduction
149(1)
What Can Be Clustered in Functional Genomics?
149(1)
What Does it Mean to Cluster?
150(1)
Hierarchy of Bioinformatics Algorithms
151(4)
Data Reduction and Filtering
155(6)
Variation filter
155(1)
Low entropy filter
156(4)
Minimum expression level filter
160(1)
Target ambiguity filter
161(1)
Self-Organizing Maps
161(8)
K-means clustering
164(5)
Finding Genes That Split Sets
169(3)
Phylogenetic-Type Trees
172(9)
Two-dimensional dendrograms
176(5)
Relevance Networks
181(8)
Other Methods
189(2)
Which Technique Should I Use?
191(4)
Determining the Significance of Findings
195(8)
Permutation testing
196(1)
Testing and training sets
197(3)
Performance metrics
200(1)
Receiver operating characteristic curves
201(2)
Genetic Networks
203(12)
What is a genetic network?
203(1)
Reverse-engineering and modeling a genetic network using limited data
204(4)
Bayesian networks for functional genomics
208(7)
Bio-Ontologies, Data Models, Nomenclature
215(34)
Ontologies
216(8)
Bio-ontology projects
218(4)
Advanced knowledge representation systems for bio-ontology
222(2)
Expressivity versus Computability
224(2)
Ontology versus Data Model versus Nomenclature
226(5)
Exploiting the explicit and implicit ontologies of the biomedical literature
228(3)
Data Model Introduction
231(8)
Nomenclature
239(8)
The unique gene identifier
243(4)
Postanalysis Challenges
247(2)
Linking to downstream biological validation
247(1)
Problems in determining the results
248(1)
From Functional Genomics to Clinical Relevance
249(8)
Electronic Medical Records
249(2)
Standardized Vocabularies for Clinical Phenotypes
251(1)
Privacy of Clinical Data
252(4)
Anonymization
253(2)
Privacy rules
255(1)
Costs of Clinical Data Acquisition
256(1)
The Near Future
257(20)
New Methods for Gene Expression Profiling
257(9)
Electronic positioning of molecules: Nanogen
259(1)
Ink-jet spotting of arrays: Agilent
260(2)
Coded microbeads bound to oligonucleotides: Illumina
262(2)
Serial Analysis of Gene Expression (Sage)
264(1)
Parallel signature sequencing on microbead arrays: Lynx
264(2)
Gel pad technology: Motorola
266(1)
Respecting the Older Generation
266(5)
The generation gap
267(1)
Separating the wheat from the chaff
267(3)
A persistent problem
270(1)
Selecting Software
271(2)
Investing in the Future of the Genomic Enterprise
273(4)
Glossary 277(6)
References 283(13)
Index 296
Extra informatie: 
Paperback / softback
326 pagina's
Januari 2005
517 gram
230 x 179 x 17 mm
MIT Press Ltd us


Levertijd: 5 tot 11 werkdagen