| Description |
1 online resource (xv, 481 pages, 16 unnumbered pages of plates) : illustrations (some color) |
| Contents |
""Contents""; ""List of Contributors""; ""Preface""; ""1 An Introduction to Next-Generation Biological Platforms""; ""Virginia Mohlere, Wenting Wang, and Ganiraju Manyam""; ""1.1 Introduction""; ""1.2 The Biology of Gene Silencing""; ""1.2.1 DNA Methylation""; ""1.2.2 RNA Interference""; ""1.3 High-Throughput Profiling""; ""1.3.1 Molecular Inversion Probe Arrays""; ""1.3.2 Array Comparative Genomic Hybridization (aCGH)""; ""1.3.3 Genome-Wide Association Studies""; ""1.3.4 Reverse-Phase Protein Array""; ""1.4 Next-Generation Sequencing""; ""1.4.1 Whole-Genome and Whole-Exome Sequencing"" |
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""1.4.2 ChIP-Seq""""1.4.3 RNA-Seq""; ""1.4.4 BS-seq""; ""1.5 NGS Data Management and Analysis""; ""1.6 Platform Integration""; ""Acknowledgments""; ""References""; ""References""; ""2 An Introduction to The Cancer Genome Atlas""; ""Bradley M. Broom and Rehan Akbani""; ""2.1 Introduction""; ""2.2 History and Goals of the TCGA Project""; ""2.3 Sample Collection and Processing""; ""2.3.1 Step 1: Tissue Collection""; ""2.3.2 Step 2: Quality Control and DNA/RNA Extraction""; ""2.3.3 Step 3: Molecular Profiling and Sequencing""; ""2.3.4 Step 4: Data Collection and Public Distribution"" |
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""2.3.5 Step 5: Data Analysis""""2.4 Data Processing, Storage, and Access""; ""2.4.1 TCGA Barcodes and UUIDs""; ""2.4.2 The Data Coordinating Center""; ""2.4.3 Data Access Matrix""; ""2.4.4 Bulk Download""; ""2.4.5 HTTP""; ""2.4.6 CGHub""; ""2.4.7 Sample and Data Relationship Format (SDRF) and Investigation Description Format (IDF) Files""; ""2.4.8 File Format""; ""2.4.9 Version""; ""2.5 Tools for Visualizing and Analyzing TCGA Data""; ""2.5.1 cBio Cancer Genomics Portal""; ""2.5.2 MBatch Portal""; ""2.5.3 Next-Generation Clustered Heat Maps""; ""2.5.4 Regulome Explorer"" |
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""2.5.5 Integrative Genome Viewer""""2.5.6 Cancer Genomics Browser""; ""2.6 Summary""; ""Acknowledgments""; ""References""; ""References""; ""3 DNA Variant Calling in Targeted Sequencing Data""; ""Wenyi Wang, Yu Fan, and Terence P. Speed""; ""3.1 Introduction""; ""3.2 Background""; ""3.2.1 Single-Nucleotide Variation""; ""3.2.2 Long Padlock Probes""; ""3.2.3 Array-Based Resequencing""; ""3.3 Sequence Robust Multiarray Analysis""; ""3.3.1 Quality Control""; ""3.3.2 Variant Calling""; ""3.4 Application of SRMA""; ""3.4.1 Candidate Gene Study for Mitochondrial Diseases"" |
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""3.4.2 Validation Results""""3.4.3 Biological Findings""; ""3.5 Conclusion""; ""Appendix""; ""References""; ""References""; ""4 Statistical Analysis of Mapped Reads from mRNA-Seq Data""; ""Ernest Turro and Alex Lewin""; ""4.1 Background""; ""4.1.1 RNA Biology""; ""4.1.2 RNA Technology""; ""4.2 Mapping and Assembly Strategies""; ""4.2.1 De Novo Assembly of the Transcriptome""; ""4.2.2 Genome-Guided Assembly of the Transcriptome""; ""4.2.3 Alignment to a Reference Transcriptome""; ""4.3 Modeling Expression Levels""; ""4.3.1 Poisson Model for Expression Quantification""; ""4.4 Normalization"" |
| Summary |
This book describes the integration of high-throughput bioinformatics data from multiple platforms to inform our understanding of the functional consequences of genomic alterations |
| Bibliography |
Includes bibliographical references and index |
| Notes |
Online resource; title from online resource (viewed June 19, 2013) |
| Subject |
Bioinformatics -- Statistical methods
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Biometry.
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Genetics -- Technique.
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Biometry
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Genetic Techniques
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biometrics.
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MEDICAL -- Biostatistics.
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COMPUTERS -- Bioinformatics.
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Biometry
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Genetics -- Technique
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| Form |
Electronic book
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| Author |
Do, Kim-Anh, 1960-
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Qin, Steven, 1972-
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Vannucci, Marina, 1966-
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| ISBN |
9781107250246 |
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1107250242 |
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9781139226448 |
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1139226444 |
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9781299707511 |
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1299707513 |
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9781107247758 |
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1107247756 |
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