Analyzing Microarray Gene Expression Data

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Analyzing Microarray Gene Expression Data

Geoffrey J. McLachlan,Kim-Anh Do,Christophe Ambroise
Analyzing Microarray Gene Expression Data Book PDF

Author : Geoffrey J. McLachlan,Kim-Anh Do,Christophe Ambroise
Publisher : John Wiley & Sons
Page : 366 pages
File Size : 45,6 Mb
Release : 2005-02-18
Category : Mathematics
ISBN : 9780471726128

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Analyzing Microarray Gene Expression Data by Geoffrey J. McLachlan,Kim-Anh Do,Christophe Ambroise Pdf

A multi-discipline, hands-on guide to microarray analysis of biological processes Analyzing Microarray Gene Expression Data provides a comprehensive review of available methodologies for the analysis of data derived from the latest DNA microarray technologies. Designed for biostatisticians entering the field of microarray analysis as well as biologists seeking to more effectively analyze their own experimental data, the text features a unique interdisciplinary approach and a combined academic and practical perspective that offers readers the most complete and applied coverage of the subject matter to date. Following a basic overview of the biological and technical principles behind microarray experimentation, the text provides a look at some of the most effective tools and procedures for achieving optimum reliability and reproducibility of research results, including: An in-depth account of the detection of genes that are differentially expressed across a number of classes of tissues Extensive coverage of both cluster analysis and discriminant analysis of microarray data and the growing applications of both methodologies A model-based approach to cluster analysis, with emphasis on the use of the EMMIX-GENE procedure for the clustering of tissue samples The latest data cleaning and normalization procedures The uses of microarray expression data for providing important prognostic information on the outcome of disease

Analysis of Microarray Gene Expression Data

Mei-Ling Ting Lee
Analysis of Microarray Gene Expression Data Book PDF

Author : Mei-Ling Ting Lee
Publisher : Springer Science & Business Media
Page : 378 pages
File Size : 53,9 Mb
Release : 2004-04-30
Category : Mathematics
ISBN : 9780792370871

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Analysis of Microarray Gene Expression Data by Mei-Ling Ting Lee Pdf

After genomic sequencing, microarray technology has emerged as a widely used platform for genomic studies in the life sciences. Microarray technology provides a systematic way to survey DNA and RNA variation. With the abundance of data produced from microarray studies, however, the ultimate impact of the studies on biology will depend heavily on data mining and statistical analysis. The contribution of this book is to provide readers with an integrated presentation of various topics on analyzing microarray data.

Microarray Gene Expression Data Analysis

Helen Causton,John Quackenbush,Alvis Brazma
Microarray Gene Expression Data Analysis Book PDF

Author : Helen Causton,John Quackenbush,Alvis Brazma
Publisher : John Wiley & Sons
Page : 176 pages
File Size : 50,9 Mb
Release : 2009-04-01
Category : Science
ISBN : 9781444311563

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Microarray Gene Expression Data Analysis by Helen Causton,John Quackenbush,Alvis Brazma Pdf

This guide covers aspects of designing microarray experiments and analysing the data generated, including information on some of the tools that are available from non-commercial sources. Concepts and principles underpinning gene expression analysis are emphasised and wherever possible, the mathematics has been simplified. The guide is intended for use by graduates and researchers in bioinformatics and the life sciences and is also suitable for statisticians who are interested in the approaches currently used to study gene expression. Microarrays are an automated way of carrying out thousands of experiments at once, and allows scientists to obtain huge amounts of information very quickly Short, concise text on this difficult topic area Clear illustrations throughout Written by well-known teachers in the subject Provides insight into how to analyse the data produced from microarrays

Analysis of Microarray Gene Expression Data

Mei-Ling Ting Lee
Analysis of Microarray Gene Expression Data Book PDF

Author : Mei-Ling Ting Lee
Publisher : Springer Science & Business Media
Page : 377 pages
File Size : 45,6 Mb
Release : 2007-05-08
Category : Science
ISBN : 9781402077883

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Analysis of Microarray Gene Expression Data by Mei-Ling Ting Lee Pdf

After genomic sequencing, microarray technology has emerged as a widely used platform for genomic studies in the life sciences. Microarray technology provides a systematic way to survey DNA and RNA variation. With the abundance of data produced from microarray studies, however, the ultimate impact of the studies on biology will depend heavily on data mining and statistical analysis. The contribution of this book is to provide readers with an integrated presentation of various topics on analyzing microarray data.

Statistical Analysis of Gene Expression Microarray Data

Terry Speed
Statistical Analysis of Gene Expression Microarray Data Book PDF

Author : Terry Speed
Publisher : CRC Press
Page : 237 pages
File Size : 47,5 Mb
Release : 2003-03-26
Category : Mathematics
ISBN : 9780203011232

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Statistical Analysis of Gene Expression Microarray Data by Terry Speed Pdf

Although less than a decade old, the field of microarray data analysis is now thriving and growing at a remarkable pace. Biologists, geneticists, and computer scientists as well as statisticians all need an accessible, systematic treatment of the techniques used for analyzing the vast amounts of data generated by large-scale gene expression studies

A Practical Approach to Microarray Data Analysis

Daniel P. Berrar,Werner Dubitzky,Martin Granzow
A Practical Approach to Microarray Data Analysis Book PDF

Author : Daniel P. Berrar,Werner Dubitzky,Martin Granzow
Publisher : Springer Science & Business Media
Page : 382 pages
File Size : 54,6 Mb
Release : 2007-05-08
Category : Science
ISBN : 9780306478154

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A Practical Approach to Microarray Data Analysis by Daniel P. Berrar,Werner Dubitzky,Martin Granzow Pdf

In the past several years, DNA microarray technology has attracted tremendous interest in both the scientific community and in industry. With its ability to simultaneously measure the activity and interactions of thousands of genes, this modern technology promises unprecedented new insights into mechanisms of living systems. Currently, the primary applications of microarrays include gene discovery, disease diagnosis and prognosis, drug discovery (pharmacogenomics), and toxicological research (toxicogenomics). Typical scientific tasks addressed by microarray experiments include the identification of coexpressed genes, discovery of sample or gene groups with similar expression patterns, identification of genes whose expression patterns are highly differentiating with respect to a set of discerned biological entities (e.g., tumor types), and the study of gene activity patterns under various stress conditions (e.g., chemical treatment). More recently, the discovery, modeling, and simulation of regulatory gene networks, and the mapping of expression data to metabolic pathways and chromosome locations have been added to the list of scientific tasks that are being tackled by microarray technology. Each scientific task corresponds to one or more so-called data analysis tasks. Different types of scientific questions require different sets of data analytical techniques. Broadly speaking, there are two classes of elementary data analysis tasks, predictive modeling and pattern-detection. Predictive modeling tasks are concerned with learning a classification or estimation function, whereas pattern-detection methods screen the available data for interesting, previously unknown regularities or relationships.

Advanced Analysis Of Gene Expression Microarray Data

Aidong Zhang
Advanced Analysis Of Gene Expression Microarray Data Book PDF

Author : Aidong Zhang
Publisher : World Scientific Publishing Company
Page : 356 pages
File Size : 40,9 Mb
Release : 2006-06-27
Category : Science
ISBN : 9789813106642

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Advanced Analysis Of Gene Expression Microarray Data by Aidong Zhang Pdf

This book focuses on the development and application of the latest advanced data mining, machine learning, and visualization techniques for the identification of interesting, significant, and novel patterns in gene expression microarray data.Biomedical researchers will find this book invaluable for learning the cutting-edge methods for analyzing gene expression microarray data. Specifically, the coverage includes the following state-of-the-art methods:• Gene-based analysis: the latest novel clustering algorithms to identify co-expressed genes and coherent patterns in gene expression microarray data sets• Sample-based analysis: supervised and unsupervised methods for the reduction of the gene dimensionality to select significant genes. A series of approaches to disease classification and discovery are also described• Pattern-based analysis: methods for ascertaining the relationship between (subsets of) genes and (subsets of) samples. Various novel pattern-based clustering algorithms to find the coherent patterns embedded in the sub-attribute spaces are discussed• Visualization tools: various methods for gene expression data visualization. The visualization process is intended to transform the gene expression data set from high-dimensional space into a more easily understood two- or three-dimensional space.

Statistical Analysis of Gene Expression Microarray Data

Terry Speed
Statistical Analysis of Gene Expression Microarray Data Book PDF

Author : Terry Speed
Publisher : CRC Press
Page : 332 pages
File Size : 55,7 Mb
Release : 2003-03-26
Category : Mathematics
ISBN : 9781135441364

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Statistical Analysis of Gene Expression Microarray Data by Terry Speed Pdf

Although less than a decade old, the field of microarray data analysis is now thriving and growing at a remarkable pace. Biologists, geneticists, and computer scientists as well as statisticians all need an accessible, systematic treatment of the techniques used for analyzing the vast amounts of data generated by large-scale gene expression studies

Methods of Microarray Data Analysis

Simon M. Lin,Kimberly F. Johnson
Methods of Microarray Data Analysis Book PDF

Author : Simon M. Lin,Kimberly F. Johnson
Publisher : Springer Science & Business Media
Page : 192 pages
File Size : 51,7 Mb
Release : 2012-12-06
Category : Science
ISBN : 9781461508731

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Methods of Microarray Data Analysis by Simon M. Lin,Kimberly F. Johnson Pdf

Microarray technology is a major experimental tool for functional genomic explorations, and will continue to be a major tool throughout this decade and beyond. The recent explosion of this technology threatens to overwhelm the scientific community with massive quantities of data. Because microarray data analysis is an emerging field, very few analytical models currently exist. Methods of Microarray Data Analysis is one of the first books dedicated to this exciting new field. In a single reference, readers can learn about the most up-to-date methods ranging from data normalization, feature selection and discriminative analysis to machine learning techniques. Currently, there are no standard procedures for the design and analysis of microarray experiments. Methods of Microarray Data Analysis focuses on two well-known data sets, using a different method of analysis in each chapter. Real examples expose the strengths and weaknesses of each method for a given situation, aimed at helping readers choose appropriate protocols and utilize them for their own data set. In addition, web links are provided to the programs and tools discussed in several chapters. This book is an excellent reference not only for academic and industrial researchers, but also for core bioinformatics/genomics courses in undergraduate and graduate programs.

Microarray Data

Shailaja R. Deshmukh,Sudha G. Purohit
Microarray Data Book PDF

Author : Shailaja R. Deshmukh,Sudha G. Purohit
Publisher : Alpha Science International, Limited
Page : 354 pages
File Size : 54,6 Mb
Release : 2007
Category : Business & Economics
ISBN : STANFORD:36105131675089

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Microarray Data by Shailaja R. Deshmukh,Sudha G. Purohit Pdf

Functional Genomics, a branch of bioinformatics, is essentially an interdisciplinary subject in which biologists, statisticians and computer experts interact to analyze the microarray data. This book caters to the needs of all the three disciplines. For biologists and computer scientists, it explains concepts of statistics and statistical inference. For Biologists and Statisticians, it provides annotated R programs to analyze microarray data. For Statisticians and Computer scientists, it explains basics of biology relevant to microarray experiment. Thus, the book will be useful to scientists from all the three disciplines, with not much knowledge of other disciplines, to analyze microarray data and interpret the results.

The Analysis of Gene Expression Data

Giovanni Parmigiani,Elizabeth S. Garett,Rafael A. Irizarry,Scott L. Zeger
The Analysis of Gene Expression Data Book PDF

Author : Giovanni Parmigiani,Elizabeth S. Garett,Rafael A. Irizarry,Scott L. Zeger
Publisher : Springer Science & Business Media
Page : 456 pages
File Size : 40,9 Mb
Release : 2006-04-11
Category : Medical
ISBN : 9780387216799

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The Analysis of Gene Expression Data by Giovanni Parmigiani,Elizabeth S. Garett,Rafael A. Irizarry,Scott L. Zeger Pdf

This book presents practical approaches for the analysis of data from gene expression micro-arrays. It describes the conceptual and methodological underpinning for a statistical tool and its implementation in software. The book includes coverage of various packages that are part of the Bioconductor project and several related R tools. The materials presented cover a range of software tools designed for varied audiences.

Methods of Microarray Data Analysis IV

Jennifer S. Shoemaker,Simon M. Lin
Methods of Microarray Data Analysis IV Book PDF

Author : Jennifer S. Shoemaker,Simon M. Lin
Publisher : Springer Science & Business Media
Page : 266 pages
File Size : 45,7 Mb
Release : 2006-01-16
Category : Medical
ISBN : 9780387230771

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Methods of Microarray Data Analysis IV by Jennifer S. Shoemaker,Simon M. Lin Pdf

As studies using microarray technology have evolved, so have the data analysis methods used to analyze these experiments. The CAMDA conference plays a role in this evolving field by providing a forum in which investors can analyze the same data sets using different methods. Methods of Microarray Data Analysis IV is the fourth book in this series, and focuses on the important issue of associating array data with a survival endpoint. Previous books in this series focused on classification (Volume I), pattern recognition (Volume II), and quality control issues (Volume III). In this volume, four lung cancer data sets are the focus of analysis. We highlight three tutorial papers, including one to assist with a basic understanding of lung cancer, a review of survival analysis in the gene expression literature, and a paper on replication. In addition, 14 papers presented at the conference are included. This book is an excellent reference for academic and industrial researchers who want to keep abreast of the state of the art of microarray data analysis. Jennifer Shoemaker is a faculty member in the Department of Biostatistics and Bioinformatics and the Director of the Bioinformatics Unit for the Cancer and Leukemia Group B Statistical Center, Duke University Medical Center. Simon Lin is a faculty member in the Department of Biostatistics and Bioinformatics and the Manager of the Duke Bioinformatics Shared Resource, Duke University Medical Center.

Methods of Microarray Data Analysis III

Kimberly F. Johnson,Simon M. Lin
Methods of Microarray Data Analysis III Book PDF

Author : Kimberly F. Johnson,Simon M. Lin
Publisher : Springer Science & Business Media
Page : 247 pages
File Size : 52,5 Mb
Release : 2003-09-30
Category : Science
ISBN : 9781402075827

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Methods of Microarray Data Analysis III by Kimberly F. Johnson,Simon M. Lin Pdf

As microarray technology has matured, data analysis methods have advanced as well. Methods Of Microarray Data Analysis III is the third book in this pioneering series dedicated to the existing new field of microarrays. While initial techniques focused on classification exercises (volume I of this series), and later on pattern extraction (volume II of this series), this volume focuses on data quality issues. Problems such as background noise determination, analysis of variance, and errors in data handling are highlighted. Three tutorial papers are presented to assist with a basic understanding of underlying principles in microarray data analysis, and twelve new papers are highlighted analyzing the same CAMDA'02 datasets: the Project Normal data set or the Affymetrix Latin Square data set. A comparative study of these analytical methodologies brings to light problems, solutions and new ideas. This book is an excellent reference for academic and industrial researchers who want to keep abreast of the state of art of microarray data analysis.

DNA Microarray Technology and Data Analysis in Cancer Research

Shaoguang Li,Dongguang Li
DNA Microarray Technology and Data Analysis in Cancer Research Book PDF

Author : Shaoguang Li,Dongguang Li
Publisher : World Scientific
Page : 131 pages
File Size : 53,7 Mb
Release : 2008
Category : Medical
ISBN : 9789812790453

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DNA Microarray Technology and Data Analysis in Cancer Research by Shaoguang Li,Dongguang Li Pdf

DNA microarray technology has become a useful technique in gene expression analysis for the development of new diagnostic tools and for the identification of disease genes and therapeutic targets for human cancers. Appropriate control for DNA microarray experiment and reliable analysis of the array data are key to performing the assay and utilizing the data correctly. The most difficult challenge has been the lack of a powerful method to analyze the data for all genes (more than 30,000 genes) simultaneously and to use the microarray data in a decision-making process. In this book, the authors describe DNA microarray technology and data analysis by pointing out current advantages and disadvantages of the technique and available analytical methods. Crucially, new ideas and analytical methods based on the authors' own experience in DNA microarray study and analysis are introduced. It is believed that this new way of interpreting and analyzing microarray data will bring us closer to success in decision-making using the information obtained through the DNA microarray technology.

Analysis of Microarray Data

Matthias Dehmer,Frank Emmert-Streib
Analysis of Microarray Data Book PDF

Author : Matthias Dehmer,Frank Emmert-Streib
Publisher : John Wiley & Sons
Page : 438 pages
File Size : 43,5 Mb
Release : 2008-09-08
Category : Medical
ISBN : 9783527622825

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Analysis of Microarray Data by Matthias Dehmer,Frank Emmert-Streib Pdf

This book is the first to focus on the application of mathematical networks for analyzing microarray data. This method goes well beyond the standard clustering methods traditionally used. From the contents: * Understanding and Preprocessing Microarray Data * Clustering of Microarray Data * Reconstruction of the Yeast Cell Cycle by Partial Correlations of Higher Order * Bilayer Verification Algorithm * Probabilistic Boolean Networks as Models for Gene Regulation * Estimating Transcriptional Regulatory Networks by a Bayesian Network * Analysis of Therapeutic Compound Effects * Statistical Methods for Inference of Genetic Networks and Regulatory Modules * Identification of Genetic Networks by Structural Equations * Predicting Functional Modules Using Microarray and Protein Interaction Data * Integrating Results from Literature Mining and Microarray Experiments to Infer Gene Networks The book is for both, scientists using the technique as well as those developing new analysis techniques.