Bioinformatics for geneticists / edited by Michael R. Barnes and Ian C. Gray.

Format:

Book

Author/Creator:

Barnes, Michael R.

Contributor:

Gray, Ian C.

Language:

English

Subjects (All):

Bioinformatics.

Genetics--Data processing.

Genetics.

Computational Biology.

Genetics--statistics & numerical data.

Medical Subjects:

Computational Biology.

Genetics--statistics & numerical data.

Physical Description:

xiv, 408 pages, 8 unnumbered pages of plates : illustrations (some color) ; 24 cm

Place of Publication:

Chichester, England ; Hoboken, NJ : Wiley, [2003]

Contents:

Chapter 1 Introduction: The Role of Genetic Bioinformatics / Michael R. Barnes, Ian C. Gray 3

1.2 Genetics in the post-genome era

the role of bioinformatics 6

1.3 Knowledge management and expansion 6

1.4 Data management and mining 6

1.5 Genetic study designs 8

1.6 Physical locus analysis 12

1.7 Selecting candidate genes for analysis 14

1.8 Progressing from candidate gene to disease-susceptibility gene 14

1.9 Comparative genetics and genomics 15

Chapter 2 Internet Resources for the Geneticist / Michael R. Barnes, Christopher Southan 21

2.2 Sub-division of biological data on the internet 23

2.3 Searching the internet for genetic information 24

2.4 Which web search engine? 24

2.5 Search syntax: the mathematics of search engine use 26

2.6 Boolean searching 27

2.7 Searching scientific literature

getting to 'state of the art' 28

2.8 Searching full-text journals 29

2.9 Searching the heart of the biological internet

sequences and genomic data 30

2.10 Nucleotide and protein sequence databases 30

2.11 Biological sequence databases

primary and secondary 31

Chapter 3 Human Genetic Variation: Databases and Concepts / Michael R. Barnes 39

3.2 Forms and mechanisms of genetic variation 43

3.3 Databases of human genetic variation 50

3.4 SNP databases 51

3.5 Mutation databases 57

3.6 Genetic marker and microsatellite databases 60

3.7 Non-nuclear and somatic mutation databases 61

3.8 Tools for SNP and mutation visualization

the genomic context 63

3.9 Tools for SNP and mutation visualization

the gene context 63

Chapter 4 Finding, Delineating and Analysing Genes / Christopher Southan 71

4.2 The evidence cascade for gene products 72

4.3 Shortcomings of the standard gene model 75

4.4 Locating known genes on the Golden Path 76

4.5 Gene portal inspection 79

4.6 Locating genes which are not present in the Golden Path 80

4.7 Analysing a novel gene 81

4.8 Comprehensive database searching 88

Section II. The Impact of Complete Genome Sequences on Genetics 93

Chapter 5 Assembling a View of the Human Genome / Colin A. Semple 95

5.2 Genomic sequence assembly 98

5.3 Annotation from a distance: the generalities 101

5.4 Annotation up close and personal: the specifics 105

5.5 Annotation: the next generation 113

Chapter 6 Mouse and Rat Genome Informatics / Judith A. Blake, Janan Eppig, Carol J. Bult 119

6.2 The model organism databases for mouse and rat 122

6.3 Mouse genetic and physical maps 124

6.4 Rat genetic and physical maps 127

6.5 Genome sequence resources 128

6.6 Comparative genomics 131

6.7 From genotype to phenotype 132

6.8 Functional genomics 135

6.9 Rodent disease models 137

Chapter 7 Genetic and Physical Map Resources

An Integrated View / Michael R. Barnes 143

7.2 Genetic maps 145

7.3 Physical maps 148

7.4 Physical contig maps 151

7.5 The role of physical and genetic maps in draft sequence curation 152

7.6 The human genome sequence

the ultimate physical map? 153

7.7 QC of genomic DNA

resolution of marker order and gap sizes 154

7.8 Tools and databases for map analysis and integration 155

Section III. Bioinformatics for Genetic Study Design 163

Chapter 8 From Linkage Peak to Culprit Gene: Following Up Linkage Analysis of Complex Phenotypes with Population-based Association Studies / Ian C. Gray 165

8.2 Theoretical and practical considerations 166

8.3 A practical approach to locus refinement and candidate gene identification 173

Chapter 9 Genetic Studies from Genomic Sequence / Michael R. Barnes 179

9.2 Defining the locus 180

9.3 Case study 1: Identification and extraction of a genomic sequence between two markers 184

9.4 Case study 2: Checking the integrity of a genomic sequence between two markers 185

9.5 Case study 3: Definition of known and novel genes across a genomic region 188

9.6 Case study 4: Candidate gene selection

building biological rationale around genes 190

9.7 Case study 5: Known and novel marker identification 195

9.8 Case study 6: Genetic/physical locus characterization and marker panel design 199

Chapter 10 SNP Discovery and PCR-based Assay Design: From In Silico Data to the Laboratory Experiment / Ellen Vieux, Gabor Marth, Pui Kwok 203

10.2 SNP identification 205

10.3 PCR primer design 207

10.4 Broader PCR assay design issues 208

10.5 Primer selection 210

10.6 Problems related to SNP assay validation 212

Chapter 11 Tools for Statistical Analysis of Genetic Data / Aruna Bansal, Peter R. Boyd, Ralph McGinnis 217

11.2 Linkage analysis 218

11.3 Association analysis 223

11.4 Haplotype Reconstruction 226

11.5 Linkage disequilibrium 229

11.6 Quantitative Trait Locus (QTL) mapping in experimental crosses 235

Section IV. Biological Sequence Analysis and Characterization 247

Chapter 12 Predictive Functional Analysis of Polymorphisms: An Overview / Michael R. Barnes 249

12.2 Principles of predictive functional analysis of polymorphisms 252

12.3 The anatomy of promoter regions and regulatory elements 257

12.4 The anatomy of genes 258

12.5 Pseudogenes and regulatory mRNA 264

12.6 Analysis of novel regulatory elements and motifs in nucleotide sequences 264

12.7 Functional analysis on non-synonymous coding polymorphisms 266

12.8 A note of caution on the prioritization of in silico predictions for further laboratory investigation 268

Chapter 13 Functional In Silico Analysis of Non-coding SNPs / Thomas Werner 273

13.2 General structure of chromatin-associated DNA 275

13.3 General functions of regulatory regions 276

13.4 Transcription Factor binding sites (TF-sites) 276

13.5 Structural elements 276

13.6 Organizational principles of regulatory regions 277

13.7 RNA processing 279

13.8 SNPs in regulatory regions 279

13.9 Evaluation of non-coding SNPs 280

13.10 SNPs and regulatory networks 281

13.11 SNPs may affect the expression of a gene only in specific tissues 281

13.12 In silico detection and evaluation of regulatory SNPs 281

13.13 Getting promoter sequences 282

13.14 Identification of relevant regulatory elements 283

13.15 Estimation of functional consequences of regulatory SNPs 284

Chapter 14 Amino Acid Properties and Consequences of Substitutions / Matthew J. Betts, Robert B. Russell 289

14.2 Protein features relevant to amino acid behaviour 292

14.3 Amino acid classifications 296

14.4 Properties of the amino acids 298

14.5 Amino acid quick reference 299

14.6 Studies of how mutations affect function 311

14.7 A summary of the thought process 313

Section V. Genetics/Genomics Interfaces 317

Chapter 15 Gene Expression Informatics and Analysis / Antoine H. C. van Kampen, Jan M. Ruijter, Barbera D. C. van Schaik, Huib N. Caron, Rogier Versteeg 319

15.2 Technologies for the measurement of gene expression 322

15.3 The Cancer Genome Anatomy Project (CGAP) 324

15.4 Processing of SAGE data 325

15.5 Integration of biological databases for the construction of the HTM 334

15.6 The Human Transcriptome Map 336

15.7 Regions of Increased Gene Expression (RIDGES) 339

Chapter 16 Proteomic Informatics / Jerome Wojcik, Alexandre Hamburger 345

16.2 Proteomic informatics 347

16.3 Experimental workflow: classical proteomics 347

16.4 Protein interaction networks 351

16.5 Building protein interaction networks 354

16.6 False negatives and false positives 354

16.7 Analysing interaction networks 355

16.8 Cell pathways 356

16.9 Prediction of protein networks 359

16.10 Assessment and validation of predictions 363

16.11 Exploiting protein networks 366

16.12 Deducing prediction rules from networks 367

Chapter 17 Concluding Remarks: Final Thoughts and Future Trends / Michael R. Barnes, Ian C.

Gray 373

17.1 How many genes? 374

17.2 Mapping the genome and gaining a view of the full depth of human variation 375

17.3 Holistic analysis of complex traits 376.

Notes:

Includes bibliographical references and index.

ISBN:

0470843934

0470843942

OCLC:

50712120