A primer of genome science:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Sunderland, Mass.
Sinauer
2009
|
| Ausgabe: | 3. ed. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XIII, 370 S. Ill., graph. Darst. |
| ISBN: | 9780878932368 |
Internformat
MARC
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| 650 | 4 | |a Gene Expression | |
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Datensatz im Suchindex
| _version_ | 1804139201776582656 |
|---|---|
| adam_text | Contents
Preface
xi
1
Genome
Projects: Organization and Objectives
1
The Core Aims of Genome Science
í
Mapping Genomes
4
Genetic Maps
4
EXERCISE
1.1
Construaing a genetic map
7
Physical Maps
8
Cytological Maps
8
Comparative Genomics
10
The Human Genome Project
13
Objectives
13
The Content of the Human Genome
16
BOX
1.1
The Ethical, Legal, and Social
Implications of the Human Genome Project
18
EXERCISE
1.2
Use the NCBI and Ensembl genome
browsers to
examine a
human disease gene
22
Internet Resources
22
BOX
1.2
GenBank Files
26
Animal Genome Projects
28
Primate Genome Projects
28
Rodent Genome Projects
30
EXERCISE
1.3
Compare the structure of a gene in
a mouse and a human
33
Other Vertebrate
Biomedical
Models
34
Animal Breeding Projects
35
Invertebrate Model Organisms
36
BOX
1.3
Managing and Distributing Genome
Data
40
Plant Genome Projects
40
Arabidopsis thaliana
40
Grasses and Legumes
44
Other Flowering Plants
46
Microbio
IGenome Projects
48
The Minimal Genome
48
Sequenced Microbial Genomes
51
EXERCISE
1.4
Compare two microbial genomes
using the CMR
53
Yeast
54
EXERCISE
1.5
Examining a gene in the
Saccharomyces Genome Database
56
Metagenomics
59
Summary
·
Discussion Questions
·
Literature
Cited
60
Vf/f
CONTENTS
Genome
Sequencing and Annotation
65
Automated
DNA
Sequencing
65
The Principle of
Sanger Sequendng 65
High-Throughput Sequencing
68
Reading Sequence Traces
68
EXERCISE
2.1
Reading a sequence trace
71
Contig Assembly
71
BOX
2.1
Pairwise Sequence Alignment
74
EXERCISE
2.2
Computing an optimal sequence
alignment
78
Emerging Sequencing Methods:
The Next Generation
79
Genome Sequencing
83
Hierarchical Sequencing
84
Shotgun Sequencing
88
BOX
2.2
Searching Sequence Databases
Using BLAST
90
Sequence Verification
94
Genome Annotation
95
EST
Sequencing
95
Ab Initio
Gene Discovery
98
BOX
2.3
Hidden Markov Models and Gene
Finding
100
Regulatory Sequences
103
Non-Protein Coding Genes
104
Structural Features of Genome Sequences
107
Functional Annotation and Clusters
of Gene Families
113
EXERCISE
2.3
Perform a BLAST search
114
Clustering of Genes by Sequence Similarity
114
Clusters of Orthologous Genes
116
Phylogenetic Classification of Genes
119
BOX
2.4
Phylogenetics
120
EXERCISE
2.4
A simple phylogenetic analysis
123
Gene Ontology
124
BOX
2.5
Gene Ontologies
126
Summary
·
Discussion Questions
·
Web Site
Exercises
·
Literature Cited
128
Genomic Variation
133
The Nature of Single Nucleotide
Polymorphisms
133
Distribution of SNPs
136
Unkage Disequilibrium and
Haplotype Maps
138
BOX
3.1
Disequilibrium between
Alíeles
at
Two Loci
138
EXERCISE
3.1
Quantifying heterozygosity
andLD
143
Applications of
SNP
Technology
146
Population Genetics
146
BOX
3.2
The Coalescent
148
Recombination Mapping
152
EXERCISE
3.2
Inferring haplotype structure
154
QTL Mapping
155
Linkage Disequilibrium Mapping
158
BOX
3.3
Case-Control Association Studies
164
BOX
3.4
Family-Based Association Tests
167
EXERCISE
3.3
Perform a case-control association
test
170
BOX
3.5
Genome-Wide Association Studies
173
SNP
Genotyping
177
SNP
Discovery
177
SNP
Genotyping
178
EXERCISE
3.4
Designing a genotyping assay for a
double polymorphism
183
High-throughput genotyping platforms
183
Haplotype phasing methods
185
Summary
·
Discussion Questions
·
Web Site
Exercises
·
Literature Cited
186
CONTENTS
IX
Gene Expression
and the Transcriptome
191
Parallel Analysis of Gene
Expression: Microarrays
191
Applications of Microarray Technology
192
Experimental Design
194
EXERCISE
4.1
Design a microarray experiment
196
Microarray Technologies
198
Labeling and Hybridization of cDNAs
205
Statistical Analysis of cDNA Microarray Data
207
EXERCISE
4.2
Calculate which genes are
differentially exposed
209
BOX
4.1
Microarray Image Processing
211
BOX
4.2
Basic Statistical Methods
214
EXERCISE
4.3
Evaluate the significance of the
following gene expression differences
217
Microarray Data Mining
220
BOX
4.3
Clustering Methods
221
EXERCISE
4.4
Perform a cluster analysis on gene
expression profiles
224
ChIP Chips and Gene Regulation
225
DNA
Applications of Microarrays
227
BOX
4.4
Motif Detection in Promoter
Sequences
228
Parallel Analysis of Gene
Expression:
RNA
Sequencing
231
Serial Analysis of Gene Expression
231
RNA-Seq
234
Single-Gene Analyses
236
Northern Blots
236
Quantitative PCR
237
Properties of
Transcriptomes
239
Microbial Transcriptomics
239
Cancer and Clinical Applications
243
Development, Physiology, and Behavior
246
Evolutionary and Ecological
Functional Genomics
248
Gene Expression Databases
252
Summary
·
Discussion Questions
·
Web Site
Exercises
·
Literature Cited
253
Proteomics and Functional Genomics
259
Functional Proteomics
259
Protein Annotation
259
EXERCISE
5.1
Structural annotation of a
protein
262
BOX
5.1
Hidden Markov Models in Domain
Profiling
264
Protein Separation and 2D-PAGE
267
Mass Spectrometry
270
EXERCISE
5.2
Identification of a protein on the
basis of a mass spectrometry profile
273
Immunochemistry
276
Protein Microarrays
277
Protein Interaction Maps
280
EXERCISE
5.3
Formulating a network of protein
interactions
281
BOX
5.2
Biological Networks in Genome
Science
283
Structural Proteomics
286
Objectives of Structural Proteomics
286
Protein Structure Determination
288
Protein Structure Prediction and Threading
291
Functional Genomics
294
Saturation Forward Genetics
295
High-Throughput Reverse Genetics
300
BOX
5.3
Transgenic Animals and Plants
304
Fine-Structure Genetics
308
EXERCISE
5.4
Designing a genetic screen
309
Genetic Fingerprinting
314
Summary
·
Discussion Questions
·
Web Site
Exercises
·
Literature Cited
317
Ό
Integrative
Genom
ics
323
Metabolomics
325
Analysis of Cellular Constituents
525
Metabolic Profiling
328
Metabolic and Biochemical Databases
331
In Silico Genomics
333
Metabolic Control Analysis
333
Systems-Level Modeling of Gene Networks
338
Summary
·
Discussion Questions
·
Literature
Cited
342
Glossary
345
List of Abbreviations
355
Index
357
|
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| discipline | Biologie |
| edition | 3. ed. |
| format | Book |
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| id | DE-604.BV035555198 |
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| indexdate | 2024-07-09T21:40:19Z |
| institution | BVB |
| isbn | 9780878932368 |
| language | English |
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| spelling | Gibson, Greg 1963- Verfasser (DE-588)138203881 aut A primer of genome science Greg Gibson ; Spencer V. Muse 3. ed. Sunderland, Mass. Sinauer 2009 XIII, 370 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Computational Biology methods Gene Expression Genome Genomics Genanalyse (DE-588)4200230-8 gnd rswk-swf Genom (DE-588)4156640-3 gnd rswk-swf Genexpression (DE-588)4020136-3 gnd rswk-swf Molekulare Bioinformatik (DE-588)4531334-9 gnd rswk-swf Genom (DE-588)4156640-3 s Molekulare Bioinformatik (DE-588)4531334-9 s DE-604 Genanalyse (DE-588)4200230-8 s 1\p DE-604 Genexpression (DE-588)4020136-3 s 2\p DE-604 Muse, Spencer V. 1966- Sonstige (DE-588)138111790 oth Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017611034&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 2\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Gibson, Greg 1963- A primer of genome science Computational Biology methods Gene Expression Genome Genomics Genanalyse (DE-588)4200230-8 gnd Genom (DE-588)4156640-3 gnd Genexpression (DE-588)4020136-3 gnd Molekulare Bioinformatik (DE-588)4531334-9 gnd |
| subject_GND | (DE-588)4200230-8 (DE-588)4156640-3 (DE-588)4020136-3 (DE-588)4531334-9 |
| title | A primer of genome science |
| title_auth | A primer of genome science |
| title_exact_search | A primer of genome science |
| title_full | A primer of genome science Greg Gibson ; Spencer V. Muse |
| title_fullStr | A primer of genome science Greg Gibson ; Spencer V. Muse |
| title_full_unstemmed | A primer of genome science Greg Gibson ; Spencer V. Muse |
| title_short | A primer of genome science |
| title_sort | a primer of genome science |
| topic | Computational Biology methods Gene Expression Genome Genomics Genanalyse (DE-588)4200230-8 gnd Genom (DE-588)4156640-3 gnd Genexpression (DE-588)4020136-3 gnd Molekulare Bioinformatik (DE-588)4531334-9 gnd |
| topic_facet | Computational Biology methods Gene Expression Genome Genomics Genanalyse Genom Genexpression Molekulare Bioinformatik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017611034&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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