10.6 USING TILING ARRAYS As we describe above, tiling arrays can be used to explore any facet of genome organization ... underlying these areas before considering the analytical approaches necessary for interpreting tiling array data.
Author: Steve Russell
Publisher: Academic Press
Using chips composed of thousands of spots, each with the capability of holding DNA molecules corresponding to a given gene, DNA microarray technology has enabled researchers to measure simultaneously gene expression across the genome. As with other large-scale genomics approaches, microarray technologies are broadly applicable across disciplines of life and biomedical sciences, but remain daunting to many researchers. This guide is designed to demystify the technology and inform more biologists about this critically important experimental technique. Cohesive overview of the technology and available platforms, followed by detailed discussion of experimental design and analysis of microarray experiments Up-to-date description of normalization methods and current methods for sample amplification and labeling Deep focus on oligonucleotide design, printing, labeling and hybridization, data acquisition, normalization, and meta-analysis Additional uses of microarray technology such as ChIP (chromatin immunoprecipitation) with hybridization to DNA arrays, microarray-based comparative genomic hybridization (CGH), and cell and tissue arrays
2.6.1 TILING ARRAYS One of the most popular types of microarrays is the tiling array. Tiling arrays are also produced in a similar manner to traditional microarrays [23, 24]. However, the probes present in the array are selected by ...
Author: Luis Rueda
Publisher: CRC Press
Microarray Image and Data Analysis: Theory and Practice is a compilation of the latest and greatest microarray image and data analysis methods from the multidisciplinary international research community. Delivering a detailed discussion of the biological aspects and applications of microarrays, the book: Describes the key stages of image processing, gridding, segmentation, compression, quantification, and normalization Features cutting-edge approaches to clustering, biclustering, and the reconstruction of regulatory networks Covers different types of microarrays such as DNA, protein, tissue, and low- and high-density oligonucleotide arrays Examines the current state of various microarray technologies, including their availability and affordability Explains how data generated by microarray experiments are analyzed to obtain meaningful biological conclusions An essential reference for academia and industry, Microarray Image and Data Analysis: Theory and Practice provides readers with valuable tools and techniques that extend to a wide range of biological studies and microarray platforms.
Oligo probes Oligo probes Figure 3.18 Exon arrays and tiling arrays. The features on a microarray chip can correspond to different aspects of the genome. In an exon array (panel A), the probes correspond to sequences in exons, ...
Author: Philip Meneely
Publisher: Oxford University Press, USA
How do we know what role a particular gene has? How do some genes control the expression of others? How do genes interact to form gene networks? With its unique integration of genetics and molecular biology, Genetic Analysis probes fascinating questions such as these, detailing how our understanding of key genetic phenomena can be used to understand biological systems. Opening with a brief overview of key genetic principles, model organisms, and epigenetics, the book goes on to explorethe use of gene mutations and the analysis of gene expression and activity. A discussion of the genetic structure of natural populations follows, before the interaction of genes during suppression and epistasis, how we study gene networks, and personalized genomics are considered. Drawing on the latest experimental tools, including microarrays, RNAi screens, and bioinformatics approaches, Genetic Analysis provides a state-of-the-art review of the field, but in a truly student-friendly manner. It uses extended case studies and text boxes to augment the narrative, taking the reader right to the forefront of contemporary research, without losing clarity of explanation and insight. We are in an age where, despite knowing so much about biological systems, we are just beginning to realise how much more there is still to understand. Genetic Analysis is the ideal guide to how we can use the awesome power of molecular genetics to further our understanding. Online Resource Centre: The Online Resource Centre to accompany Genetic Analysis features the following resources for teachers and students: For students: * Topical updates - key updates on topics or tools presented in the book, to keep you up-to-date with the latest developments in the field. * Additional case studies and text boxes to complement and add to those found in the book. * Practice problems, to test the reader's knowledge of the concepts presented, and help to master them. For registered adopters ofthe book: * Figures from the book in electronic format, ready to download. * Journal clubs - suggested papers and discussion questions linked to topics covered in the book.
Generally speaking, tiling arrays differ from microarrays in two ways. (1) A traditional microarray provides a technology for test procedures that utilize only part of particular chromosome, but applications of tiling arrays are not ...
Author: Charles J Mode
Publisher: World Scientific
The scope of this book is the field of evolutionary genetics. The book contains new methods for simulating evolution at the genomic level. It sets out applications using up to date Monte Carlo simulation methods applied in classical population genetics, and sets out new fields of quantifying mutation and selection at the Mendelian level. A serious limitation of Wright-Fisher process, the assumption that population size is constant, motivated the introduction of self regulating branching processes in this book. While providing a short review of the principles of probability and its application and using computer intensive methods whilst applying these principles, this book explains how it is possible to derive new formulas expressed in terms of matrix algebra providing new insights into the classical Wright-Fisher processes of evolutionary genetics. Also covered are the development of new methods for studying genetics and evolution, simulating nucleotide substitutions of a DNA molecule and on self regulating branching processes. Components of natural selection are studied in terms of reproductive success of each genotype whilst also studying the differential ability of genotypes to compete for resources and sexual selection. The concept of the gene is also reviewed in this book, and it provides a current definition of a gene based on very recent experiments with micro-array technologies. A development of stochastic models for simulating the evolution of model genomes concludes the studies in this book. Deserving of a place on the book shelves of workers in biomathematics, applied probability, stochastic processes and statistics, as well as in bioinformatics and phylogenetics, it will also be relevant to those interested in computer simulation, and evolutionary biologists interested in quantitative methods. Contents:An Introduction to Mathematical Probability with Applications in Mendelian GeneticsLinkage and Recombination at Multiple LociLinkage and Recombination in Large Random Mating Diploid Populations Random Mating Diploid PopulationsTwo Allele Wright-Fisher Process with Mutation and SelectionMultitype Gamete Sampling Processes, Generation of Random Numbers and Monte Carlo Simulation MethodsNucleotide Substitution Models Formulated as Markov Processes in Continuous TimeMixtures of Markov Processes as Models of Nucleotide Substitutions at Many SitesComputer Implementations and Applications of Nucleotide Substitution Models at Many Sites — Other Non-SNP Types of MutationGenealogies, Coalescence and Self-Regulating Branching ProcessesEmergence, Survival and Extinction of Mutant Types in Populations of Self Replicating Individuals Evolving From Small Founder PopulationsTwo Sex Multitype Self Regulating Branching Processes in Evolutionary GeneticsMultitype Self-Regulatory Branching Process and the Evolutionary Genetics of Age Structured Two Sex PopulationsAn Overview of the History of the Concept of a Gene and Selected Topics in Molecular GeneticsDetecting Genomic Signals of Selection and the Development of Models for Simulating the Evolution of GenomesSuggestions for Further Research, Reading and Viewing Readership: Professionals, researchers in mathematical and theoretical genetics and biology, graduate students in applied stochastic processes. Keywords:Mutation;Selection;Genes;Genomes;Stochastic Processes;Self Regulating Branching Processes;Models of GenomesKey Features:Provides many examples of applying Monte Carlo simulation methods to models that are not tractable mathematicallyRaises the study of evolution to new levels by using computer intensive methods when compared to classical and widely read population genetics books such as those by Ewens and Hartl and ClarkAll models, rooted within a formal framework of stochastic processes, enable any reader to write code in a programming language of his choice, to duplicate any of the experiments reported in the bookReviews: "Evolutionary biologists today need enough mathematical training to be able to assess the power and limits of evolutionary genetic models and to develop theories and models themselves. This book, based on very extensive—and impressive—research work, serves that purpose." Mathematical Reviews
Genomic tiling arrays use PCR amplicons or short oligonucleotide probes to tile the non-repetitive DNA sequence of a genome in an unbiased fashion for the purposes of detecting novel genomic features. Specifically, they can be used for ...
Author: Joao Carlos Setubal
This book constitutes the refereed proceedings of the Brazilian Symposium on Bioinformatics, BSB 2005, held in Sao Leopoldo, Brazil in July 2005. The 15 revised full papers and 10 revised extended abstracts presented together with 3 invited papers were carefully reviewed and selected from 55 submissions. The papers address a broad range of current topics in computational biology and bioinformatics.
Similar to gene-oriented arrays, epigenomic microarrays are easy-to-handle tools in comparison to tiling arrays and ... However, for identification of the complete set of epigenomic features of an organism, a tiling-array platform is ...
Author: Anton Buzdin
Publisher: Springer Science & Business Media
Several approaches, such as microarray hybridization, have become extremely popular tools for specialists in biochemistry and biomedicine, while the potential of many other advantageous techniques seems to be underestimated. Written by an international team of authors, this book details the current state-of-art in hybridization techniques. Coverage includes experimental protocols along with comprehensive and detailed method descriptions.
Promoter Tiling Arrays Tiling arrays use photolithographic technology in which short probes span the genome with high specificity and high resolution. This type of tiling array is commercially available through NimbleGen and Affymetrix, ...
Author: Shaun D. McCullough
Publisher: Academic Press
Toxicoepigenetics: Core Principles and Applications examines the core aspects of epigenetics, including chromatin biology, DNA methylation, and non-coding RNA, as well as fundamental techniques and considerations for studying each of these mechanisms of epigenetic regulation. Although its integration into the field of toxicology is in its infancy, epigenetics have taken center stage in the study of diseases such as cancer, diabetes, and neurodegeneration. Increasing the presence of epigenetics in toxicological research allows for a more in-depth understanding of important aspects of toxicology such as the role of the environment and lifestyle influencing the individual susceptibility to these effects and the trans-generational transmission of these health effects and susceptibilities. Methods chapters are included to help improve efficacy and efficiency of protocols in both the laboratory and the classroom. Toxicoepigenetics: Core Principles and Applications is an essential book for researchers and academics using epigenetics in toxicology research and study. Introduces the fundamental principles and practices for understanding the role of the epigenome in toxicology Presents the foundation of epigenetics for toxicologists with a broad range of backgrounds Discusses the incorporation of epigenetics and epigenomics into current toxicological studies and interpretation of epigenetic data in toxicological applications
8.2.3 GeneChip exon arrays To focus on increasing the detection capability of exons within each gene, Affymetrix Inc. has developed an exon array; ... Overcoming these limitations motivated the development of tiling arrays (see below).
Author: Carsten Wiuf
Publisher: Oxford University Press
A collection of chapters from carefully chosen experts covering the theory behind the complex mathematical, statistical, and bioinformatics tools needed to extract, handle, and process data and their application to real data.
Normalization procedures in Subheading 3.3. assume that the data from all arrays have similar distributions. This may not be true for large genomes. In typical tiling array designs, probes for different chromosomal segments are placed ...
Author: Michael J. Korenberg
Publisher: Springer Science & Business Media
In this new volume, renowned authors contribute fascinating, cutting-edge insights into microarray data analysis. Included in this innovative book includes are in-depth looks intopresentations of genomic signal processing, artificial neural network use for microarray data analysis, signal processing and design of microarray time series experiments, application of regression methods, gene expression sprofiles and prognostic markers for primary breast cancer, and factors affecting the cross-correlation of gene expression profiles. Also detailed are use of tiling arrays for large genomes analysis using tiling arrays, acomparative genomic hybridization data on cDNA microarrays, integrated high-resolution genome-wide analysis of gene dosage and gene expression in human brain tumors, gene and MeSH ontology, and predicting survival prediction in follicular lymphoma using tissue microarrays. The protocols follow the successful Methods in Molecular Biology"!series format, offering step-by-step instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding pitfalls
though the Danzer tiling array is void of grating lobes over a very wide bandwidth, its peak sidelobe levels are ... in arrays based on other comparable portions of the tilings, and for the most part, aperiodic tiling arrays in general.
Author: Frank Gross
Publisher: McGraw Hill Professional
Category: Technology & Engineering
The state of the art in antenna design and engineering Edited by one of the world's foremost authorities on smart antennas and featuring contributions from global experts, Frontiers in Antennas discusses the latest advances in antenna design and engineering. This pioneering guide deals primarily with frontier antenna designs and frontier numerical methods. Many of the concepts presented have emerged within the last few years and are still in a rapid state of development. Each chapter provides in-depth details on a unique and modern antenna technology. Frontiers in Antennas covers: Ultra-wideband antenna arrays using fractal, polyfractal, and aperiodic geometries Smart antennas using evolutionary signal processing methods The latest developments in Vivaldi antenna arrays Effective media models applied to artificial magnetic conductors and high impedance surfaces Novel developments in metamaterial antennas Biological antenna design methods using genetic algorithms Contact and parasitic methods applied to reconfigurable antennas Antennas in medicine: ingestible capsule antennas using conformal meandered methods Leaky-wave antennas Plasma antennas which can electronically appear and disappear Numerical methods in antenna modeling using time, frequency, and conformal domain decomposition methods