Introduction: The Role of Genetic Bioinformatics / Michael R. Barnes, Ian C. Gray -- Genetics in the post-genome era--the role of bioinformatics -- Knowledge management and expansion -- Data management and mining -- Genetic study designs -- Physical locus analysis -- Selecting candidate genes for analysis -- Progressing from candidate gene to disease-susceptibility gene -- Comparative genetics and genomics -- Internet Resources for the Geneticist / Michael R. Barnes, Christopher Southan -- Sub-division of biological data on the internet -- Searching the internet for genetic information -- Which web search engine? -- Search syntax: the mathematics of search engine use -- Boolean searching -- Searching scientific literature--getting to 'state of the art' -- Searching full-text journals -- Searching the heart of the biological internet--sequences and genomic data -- Nucleotide and protein sequence databases -- Biological sequence databases--primary and secondary -- Human Genetic Variation: Databases and Concepts / Michael R. Barnes -- Forms and mechanisms of genetic variation -- Databases of human genetic variation -- SNP databases -- Mutation databases -- Genetic marker and microsatellite databases -- Non-nuclear and somatic mutation databases -- Tools for SNP and mutation visualization--the genomic context -- Tools for SNP and mutation visualization--the gene context -- Finding, Delineating and Analysing Genes / Christopher Southan -- The evidence cascade for gene products -- Shortcomings of the standard gene model -- Locating known genes on the Golden Path -- Gene portal inspection -- Locating genes which are not present in the Golden Path -- Analysing a novel gene -- Comprehensive database searching -- The Impact of Complete Genome Sequences on Genetics -- Assembling a View of the Human Genome / Colin A. Semple -- Genomic sequence assembly -- Annotation from a distance: the generalities -- Annotation up close and personal: the specifics -- Annotation: the next generation -- Mouse and Rat Genome Informatics / Judith A. Blake, Janan Eppig, Carol J. Bult -- The model organism databases for mouse and rat -- Mouse genetic and physical maps -- Rat genetic and physical maps -- Genome sequence resources -- Comparative genomics -- From genotype to phenotype -- Functional genomics -- Rodent disease models -- Genetic and Physical Map Resources--An Integrated View / Michael R. Barnes -- Genetic maps -- Physical maps -- Physical contig maps -- The role of physical and genetic maps in draft sequence curation -- The human genome sequence--the ultimate physical map? -- QC of genomic DNA--resolution of marker order and gap sizes -- Tools and databases for map analysis and integration -- Bioinformatics for Genetic Study Design -- From Linkage Peak to Culprit Gene: Following Up Linkage Analysis of Complex Phenotypes with Population-based Association Studies / Ian C. Gray -- Theoretical and practical considerations -- A practical approach to locus refinement and candidate gene identification -- Genetic Studies from Genomic Sequence / Michael R. Barnes -- Defining the locus -- Case study 1: Identification and extraction of a genomic sequence between two markers -- Case study 2: Checking the integrity of a genomic sequence between two markers -- Case study 3: Definition of known and novel genes across a genomic region -- Case study 4: Candidate gene selection--building biological rationale around genes -- Case study 5: Known and novel marker identification -- Case study 6: Genetic/physical locus characterization and marker panel design -- SNP Discovery and PCR-based Assay Design: From In Silico Data to the Laboratory Experiment / Ellen Vieux, Gabor Marth, Pui Kwok -- SNP identification -- PCR primer design -- Broader PCR assay design issues -- Primer selection -- Problems related to SNP assay validation -- Tools for Statistical Analysis of Genetic Data / Aruna Bansal, Peter R. Boyd, Ralph McGinnis -- Linkage analysis -- Association analysis -- Haplotype Reconstruction -- Linkage disequilibrium -- Quantitative Trait Locus (QTL) mapping in experimental crosses -- Biological Sequence Analysis and Characterization -- Predictive Functional Analysis of Polymorphisms: An Overview / Michael R. Barnes -- Principles of predictive functional analysis of polymorphisms -- The anatomy of promoter regions and regulatory elements -- The anatomy of genes -- Pseudogenes and regulatory mRNA -- Analysis of novel regulatory elements and motifs in nucleotide sequences -- Functional analysis on non-synonymous coding polymorphisms -- A note of caution on the prioritization of in silico predictions for further laboratory investigation -- Functional In Silico Analysis of Non-coding SNPs / Thomas Werner -- General structure of chromatin-associated DNA -- General functions of regulatory regions -- Transcription Factor binding sites (TF-sites) -- Structural elements -- Organizational principles of regulatory regions -- RNA processing -- SNPs in regulatory regions -- Evaluation of non-coding SNPs -- SNPs and regulatory networks -- SNPs may affect the expression of a gene only in specific tissues -- In silico detection and evaluation of regulatory SNPs -- Getting promoter sequences -- Identification of relevant regulatory elements -- Estimation of functional consequences of regulatory SNPs -- Amino Acid Properties and Consequences of Substitutions / Matthew J. Betts, Robert B. Russell -- Protein features relevant to amino acid behaviour -- Amino acid classifications -- Properties of the amino acids -- Amino acid quick reference -- Studies of how mutations affect function -- A summary of the thought process -- Genetics/Genomics Interfaces -- Gene Expression Informatics and Analysis / Antoine H. C. van Kampen, Jan M. Ruijter, Barbera D. C. van Schaik, Huib N. Caron, Rogier Versteeg -- Technologies for the measurement of gene expression -- The Cancer Genome Anatomy Project (CGAP) -- Processing of SAGE data -- Integration of biological databases for the construction of the HTM -- The Human Transcriptome Map -- Regions of Increased Gene Expression (RIDGES) -- Proteomic Informatics / Jerome Wojcik, Alexandre Hamburger -- Proteomic informatics -- Experimental workflow: classical proteomics -- Protein interaction networks -- Building protein interaction networks -- False negatives and false positives -- Analysing interaction networks -- Cell pathways -- Prediction of protein networks -- Assessment and validation of predictions -- Exploiting protein networks -- Deducing prediction rules from networks -- Concluding Remarks: Final Thoughts and Future Trends / Michael R. Barnes, Ian C. Gray -- How many genes? -- Mapping the genome and gaining a view of the full depth of human variation -- Holistic analysis of complex traits.
- Language: eng
- Physical Description: xiv, 408 p. : ill. ; 24 cm.
- Edition Info: (PBK.)
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