DNA microarrays. Volume 411, Part B, Databases and statistics / edited by Alan Kimmel & Brian Oliver.

Contributor(s): Kimmel, Alan R | Oliver, Brian, 1959-
Material type: TextTextSeries: Methods in enzymology: volume 411, pt. B.Publisher: Amsterdam ; San Diego : Elsevier/Academic Press, ©2006Description: 1 online resource (xxxvi, 469) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9780080464664; 0080464661; 0121828166; 9780121828165Other title: Databases and statisticsSubject(s): DNA microarrays | DNA | Oligonucleotide Array Sequence Analysis -- methods | Oligonucleotide Array Sequence Analysis -- statistics & numerical data | Gene Expression Profiling -- methods | SCIENCE -- Life Sciences -- Biochemistry | DNA | DNA microarrays | dna | dna probes | dna libraries | databanken | databases | Nucleic AcidsGenre/Form: Electronic books. Additional physical formats: Print version:: DNA microarrays. pt. B, Databases and statistics.DDC classification: 572/.7 LOC classification: QP601 | .C733eb vol. 411Online resources: Click here to access online
Contents:
Cover Page; Table of Contents; Contributors to Volume 411; Volumes in Series; Chapter 1: RNA Extraction for Arrays; Introduction; Blood as a Biological Specimen; Overview of the LeukoLOCK Procedure for Isolation of RNA from Whole Blood Samples; Use of Solid Tissues for Gene Expression Analysis; RNA Quality Measurements for Microarray Analysis; Conclusion; Acknowledgments; References; Chapter 2: Analyzing Micro-RNA Expression Using Microarrays; Introduction; Micro-RNAs Are Important Factors in Human Cancer; Focus of This Chapter; Microarray Platforms.
MiRNA Preparation for Analysis on MicroarraysAnalysis of miRNA Microarray Results; Methods of Normalization for miRNA Microarray Experiments; Case Study: miRNA Microarray Expression Analysis of Human Lung and Placental Tissues; Scanning and Data Extraction; Sample Size Calculation; Calculation of Array-Specific Thresholds; Global Normalization; Statistical Differential Analysis; Hierarchical Clustering; Conclusion; Acknowledgments; References; Chapter 3: Troubleshooting Microarray Hybridizations; Introduction; General Considerations; Printing; Sample Preparation and Labeling.
Background FluorescenceHybridization Quality Assessment; Concluding Remarks; Acknowledgments; Internet Resources; References; Chapter 4: Use of External Controls in Microarray Experiments; Introduction; Description and Availability of External Controls; Assesment of Array Performance Using External RNA Controls; Methods for Synthesis and Utilization of External RNA Controls; Evaluation of Data Analysis Methodology Using Spike-In Data Sets; Concluding Remarks; Acknowledgments; References; Chapter 5: Standards in Gene Expression Microarray Experiments; Introduction; Variability.
A Digression: Traceability, Validation, and UncertaintyStandards in Traceability, Validation, and Uncertainty for DNA Microarray Gene Expression Profiles; Data Exchange Standards; Standards in the Gene Expression Process Model; The Future; References; Chapter 6: Scanning Microarrays: Current Methods and Future Directions; Introduction; Overview of the Scanning Process; User-Controlled Parameters; Instrumentation/Hardware Effects; Alternative Scanning Technologies Provide Advantages; Specific Considerations for Multiple Slide, Multiple Scanner, and/or Multiple Laboratory Experiments.
ConclusionsAcknowledgments; References; Chapter 7: An Introduction to BioArray Software Environment; Introduction; Getting Started; The Basics of BASE; Working with BASE; References; Chapter 8: Bioconductor: An Open Source Framework for Bioinformatics and Computational Biology; Introduction: Bioconductor in Brief; Technical Details; Array Preprocessing; Addressing Multiple Comparisons; Conclusions: Data Analysis for High-Throughput Biology and Bioconductor; Acknowledgment; References; Chapter 9: TM4 Microarray Software Suite; Introduction; MADAM; Spotfinder; Spotfinder Protocol Description.
Summary: Modern DNA microarray technologies have evolved over the past 25 years to the point where it is now possible to take many million measurements from a single experiment. These two volumes, Parts A & B in the Methods in Enzymology series provide methods that will shepard any molecular biologist through the process of planning, performing, and publishing microarray results. Part A starts with an overview of a number of microarray platforms, both commercial and academically produced and includes wet bench protocols for performing traditional expression analysis and derivative techniques such as detection of transcription factor occupancy and chromatin status. Wet-bench protocols and troubleshooting techniques continue into Part B. These techniques are well rooted in traditional molecular biology and while they require traditional care, a researcher that can reproducibly generate beautiful Northern or Southern blots should have no difficulty generating beautiful array hybridizations. Data management is a more recent problem for most biologists. The bulk of Part B provides a range of techniques for data handling. This includes critical issues, from normalization within and between arrays, to uploading your results to the public repositories for array data, and how to integrate data from multiple sources. There are chapters in Part B for both the debutant and the expert bioinformatician. Provides an overview of platforms Includes experimental design and wet bench protocols. Presents statistical and data analysis methods, array databases, data visualization and meta analysis.
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Modern DNA microarray technologies have evolved over the past 25 years to the point where it is now possible to take many million measurements from a single experiment. These two volumes, Parts A & B in the Methods in Enzymology series provide methods that will shepard any molecular biologist through the process of planning, performing, and publishing microarray results. Part A starts with an overview of a number of microarray platforms, both commercial and academically produced and includes wet bench protocols for performing traditional expression analysis and derivative techniques such as detection of transcription factor occupancy and chromatin status. Wet-bench protocols and troubleshooting techniques continue into Part B. These techniques are well rooted in traditional molecular biology and while they require traditional care, a researcher that can reproducibly generate beautiful Northern or Southern blots should have no difficulty generating beautiful array hybridizations. Data management is a more recent problem for most biologists. The bulk of Part B provides a range of techniques for data handling. This includes critical issues, from normalization within and between arrays, to uploading your results to the public repositories for array data, and how to integrate data from multiple sources. There are chapters in Part B for both the debutant and the expert bioinformatician. Provides an overview of platforms Includes experimental design and wet bench protocols. Presents statistical and data analysis methods, array databases, data visualization and meta analysis.

Cover Page; Table of Contents; Contributors to Volume 411; Volumes in Series; Chapter 1: RNA Extraction for Arrays; Introduction; Blood as a Biological Specimen; Overview of the LeukoLOCK Procedure for Isolation of RNA from Whole Blood Samples; Use of Solid Tissues for Gene Expression Analysis; RNA Quality Measurements for Microarray Analysis; Conclusion; Acknowledgments; References; Chapter 2: Analyzing Micro-RNA Expression Using Microarrays; Introduction; Micro-RNAs Are Important Factors in Human Cancer; Focus of This Chapter; Microarray Platforms.

MiRNA Preparation for Analysis on MicroarraysAnalysis of miRNA Microarray Results; Methods of Normalization for miRNA Microarray Experiments; Case Study: miRNA Microarray Expression Analysis of Human Lung and Placental Tissues; Scanning and Data Extraction; Sample Size Calculation; Calculation of Array-Specific Thresholds; Global Normalization; Statistical Differential Analysis; Hierarchical Clustering; Conclusion; Acknowledgments; References; Chapter 3: Troubleshooting Microarray Hybridizations; Introduction; General Considerations; Printing; Sample Preparation and Labeling.

Background FluorescenceHybridization Quality Assessment; Concluding Remarks; Acknowledgments; Internet Resources; References; Chapter 4: Use of External Controls in Microarray Experiments; Introduction; Description and Availability of External Controls; Assesment of Array Performance Using External RNA Controls; Methods for Synthesis and Utilization of External RNA Controls; Evaluation of Data Analysis Methodology Using Spike-In Data Sets; Concluding Remarks; Acknowledgments; References; Chapter 5: Standards in Gene Expression Microarray Experiments; Introduction; Variability.

A Digression: Traceability, Validation, and UncertaintyStandards in Traceability, Validation, and Uncertainty for DNA Microarray Gene Expression Profiles; Data Exchange Standards; Standards in the Gene Expression Process Model; The Future; References; Chapter 6: Scanning Microarrays: Current Methods and Future Directions; Introduction; Overview of the Scanning Process; User-Controlled Parameters; Instrumentation/Hardware Effects; Alternative Scanning Technologies Provide Advantages; Specific Considerations for Multiple Slide, Multiple Scanner, and/or Multiple Laboratory Experiments.

ConclusionsAcknowledgments; References; Chapter 7: An Introduction to BioArray Software Environment; Introduction; Getting Started; The Basics of BASE; Working with BASE; References; Chapter 8: Bioconductor: An Open Source Framework for Bioinformatics and Computational Biology; Introduction: Bioconductor in Brief; Technical Details; Array Preprocessing; Addressing Multiple Comparisons; Conclusions: Data Analysis for High-Throughput Biology and Bioconductor; Acknowledgment; References; Chapter 9: TM4 Microarray Software Suite; Introduction; MADAM; Spotfinder; Spotfinder Protocol Description.

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