A Beginner’s Guide to Microarrays

Buch | Softcover

347 Seiten

2012 | Softcover reprint of the original 1st ed. 2003
Springer-Verlag New York Inc.
978-1-4613-4684-5 (ISBN)

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A Beginner's Guide to Microarrays addresses two audiences - the core facility manager who produces, hybridizes, and scans arrays, and the basic research scientist who will be performing the analysis and interpreting the results. User friendly coverage and detailed protocols are provided for the technical steps and procedures involved in many facets of microarray technology, including:
-Cleaning and coating glass slides,
-Designing oligonucleotide probes,
-Constructing arrays for the detection and quantification of different bacterial species,
-Preparing spotting solutions,
-Troubleshooting spotting problems,
-Setting up and running a core facility,
-Normalizing background signal and controlling for systematic variance,
-Designing experiments for maximum effect,
-Analyzing data with statistical procedures,
-Clustering data with machine-learning protocols.

1 Slide Coating And DNA immobilization Chemistries.- Glass Properties.- Glass Cleaning.- Slide Coating Chemistries.- Dna Immobilization Chemistries.- Surface Analysis Methods.- Summary.- References.- 2 Diagnostic Oligonucleotide Micro Arrays For Microbiology.- Scheme of The Experimental Approach.- Sources of Variation.- Establishment of a Sequence Database.- Oligo Length And Melting Temperature (Tm); Designing Oligo Sets Tuned To Work Together.- Oligo Set Design.- Choice Of Oligo/Surface Binding Chemistry.- Array Printing.- Target Preparation.- Hybridisation.- Scanning.- Data Analysis.- Applications In Microbial Identification.- Acknowledgements.- Links Related To Dlagnostic Microbial Microarrays.- Reference List.- 3 Printing Technologies And Microarray Manufacturing Techniques: Making The Perfect Microarray.- Microarray Manufacturing.- Comparing Printing Technologies.- Conclusions.- Acknowledgments.- Reference List.- 4 Arrays For The Masses — Setting Up a Microarray Core Facility.- Preface.- Hedco/Oregon Cancer Institute Spotted Microarray Core at Ohsu.- Core Set-Up.- Array Printing.- The Printer.- Slides.- Amplification.- Printing The Array.- Hybridization.- Scanner.- Other Equipment.- Conclusion.- References.- 5 Microarraydatanormalization: The Art And Science Of Overcoming Technical Variance To Maximize The Detection Of Biologic Variance.- Normalization: Correcting For Technical Variance In Order To Study Biological Variation.- Single Channel Data Normalizations.- Normalizations Of Two-Channel Data.- The Role Of Experimental Design In The Removal Of Technical Variance.- Gene-Specific Normalizations And Clustering.- References.- 6 Experimental Design And Data Analysis.- Measuring RNA.- Fold Change Significance.- Variance.- Experimental Design.- Variance andFold-Change.- Affymetrix Data.- Working With More Than Two Groups.- Functional Grouping.- Using Excel.- Acknowledgements.- References.- 7 Microarray Experiment Design And Statistic Analysis.- Designing Amicroarray Experiment.- General Procedures For Statistical Analysis Of Microarray Data.- Multiple Hypothesis Testing In Microarray Experiments.- Methods Based On P Value Adjustment.- Analysis Of Variance.- Summary Of The Chapter.- Some Useful Online Sources For Microarray Analysis.- References.- 8 Strategies For Clustering, Classifying Integrating, Standardizing And Visualizing Microarray Gene Expression Data.- Microarray Gene Expression Matrix.- Distance Functions.- Unsupervised Analysis And Clustering Of Microarray Data.- Methods For Validating Unsupervised Analysis.- Supervised Microarray Data Analysis.- Nearest Neighbors.- Support Vector Machines.- Methods To Improve Classifier Performance.- Genetic and Biochemical Networks.- Additional Methods For Microarray Data Analysis.- Microarray Data Visualization.- Microarray Data Standardization And Integration.- Microarray Gene Expression Markup Language (MAGE-ML).- Microarray Data Repositories.- Challenges In Microarray Gene Expression Data Analysis.- Conclusions.- References.

Zusatzinfo	XVI, 347 p.
Verlagsort	New York, NY
Sprache	englisch
Maße	155 x 235 mm
Themenwelt	Informatik ► Theorie / Studium ► Algorithmen
	Naturwissenschaften ► Biologie ► Biochemie
	Naturwissenschaften ► Biologie ► Evolution
	Weitere Fachgebiete ► Land- / Forstwirtschaft / Fischerei
ISBN-10	1-4613-4684-3 / 1461346843
ISBN-13	978-1-4613-4684-5 / 9781461346845
Zustand	Neuware