Analysis of microarray data : a network-based approach

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. This text provides a first-time comprehensive review and analysis of the state of the art in clinical applications of DNA microarray data in cancer diagnostics. The acclaimed author, an international authority in the field, reviews published clinical trials for ten common cancer types. Moreover, the text provides a meta-analysis of these trials to highlight where the results concur. The author begins with a discussion of the state of DNA microarray technology, emphasizing important aspects of data analysis. Emerging technologies within the field of DNA microarrays are presented. Next, readers learn the statistical analysis techniques needed to interpret the data. Finally, the author examines some major human cancer types where microarrays have been applied with success. The author concludes, based on the evidence and his own studies in the field, that the results are so convincing for several cancer types that DNA microarrays are ready to be deployed in clinical practice.

The text provides many features for researchers and clinicians who want to use microarrays as a hands-on diagnostic tool, including: Examples and mini-cases that illustrate real-world applications, Further reading suggestions in each chapter to facilitate continued investigation of particular topics, Detailed recipes and software code for executing the techniques and analysis described in the text, Accessible, straightforward presentations that do not presume special training in statistics or bioinformatics. With the promise of DNA microarrays leading to more accurate cancer diagnoses, this text is an invaluable guide that opens the door to better care for cancer patients.

About the Author:
SteenKnudsen, PhD, is Director of Research at the Medical Prognosis Institute

Interest in microarrays has increased considerably in the last ten years. This increase in the use of microarray technology has led to the need for good standards of microarray experimental notation, data representation, and the introduction of standard experimental controls, as well as standard data normalization and analysis techniques. Statistics for Microarrays: Design, Analysis and Inference is the first book that presents a coherent and systematic overview of statistical methods in all stages in the process of analysing microarray data – from getting good data to obtaining meaningful results.

• Provides an overview of statistics for microarrays, including experimental design, data preparation, image analysis, normalization, quality control, and statistical inference.
• Features many examples throughout using real data from microarray experiments.
• Computational techniques are integrated into the text.
• Takes a very practical approach, suitable for statistically-minded biologists.
• Supported by a Website featuring colour images, software, and data sets.

Primarily aimed at statistically-minded biologists, bioinformaticians, biostatisticians, and computer scientists working with microarray data, the book is also suitable for postgraduate students of bioinformatics.

Authored by an international authority in the field,Cancer Diagnostics with DNA Microarrays is a complete reference work on the rapidly growing use of DNA microarray data in the diagnosis of and treatment planning for a large number of human cancers. Uniquely deals with direct clinical application of microarray data to oncology diagnosis, leading to more effective diagnosis of and clearer treatment regimens for a wide range of human cancers Offers clinicians summary presentation of state-of-the-art science of DNA microarrays Each chapter includes bibliographic and further reading suggestions Easily accessible, assuming no special training in statistics or bioinformatics Replete with examples and mini-cases, Cancer Diagnostics with DNA Microarrays offers cancer researchers in private, pharmacologic, and governmental institutions, biomedical statisticians, and practicing oncologists concise, thoughtfully authored guidance on the use of microarray data and analysis as clinical tools. The text carefully addresses the needs of end users -- researchers and physicians -- using microarrays as a tool to be applied in common clinical situations, and is of interest for students in medicine and biology and professionals in health care as well. Interest in microarrays has increased considerably in the last ten years. This increase in the use of microarray technology has led to the need for good standards of microarray experimental notation, data representation, and the introduction of standard experimental controls, as well as standard data normalization and analysis techniques. This book is the first book that presents a coherent and systematic overview of statistical methods in all stages in the process of analysing microarray data, from getting good data to obtaining meaningful results. Primarily aimed at statistically-minded biologists, bioinformaticians, biostatisticians, and computer scientists working with microarray data, the book is also suitable for postgraduate students of bioinformatics. In this unique presentation of a revolutionary field of science, the first section introduces the domains of application for genomics and bioinformatics, such as sequencing and the comparative sequence analysis of model organisms, investigating genetically influenced diseases, the development of new active substances, agri-food and environmental genomics. There then follows an overview of current topics central to DNA technologies, proteomics, metabolomics and bioinformatics, including such hot topics as DNA chip fabrication, yeast two hybrid analysis, tools for gene expression studies, metabolic networks and systems biology. The whole is rounded off by four chapters on the ethical, legal and social aspects of this sensitive topic. Written by leading experts from industry and academia, this first single comprehensive resource addresses recent developments in next generation DNA sequencing technology and their impact on genome research, drug discovery and health care. As such, it presents a detailed comparative analysis of commercially available platforms as well as insights into alternative, emerging sequencing techniques. In addition, the book not only covers the principles of DNA sequencing techniques but also social, ethical and commercial aspects, the concept of personalized medicine and a five-year perspective of DNA sequencing.

written By Leading Experts From Industry And Academia, This Comprehensive Resource Addresses Recent Developments In Next Generation Dna Sequencing Technology And Their Impact On Genome Research, Drug Discovery And Health Care. As Such, It Presents A Detailed Comparative Analysis Of Commercially Available Platforms As Well As Insights Into Alternative, Emerging Sequencing Techniques. In Addition, The Book Not Only Covers The Principles Of Dna Sequencing Techniques But Also Social, Ethical And Commercial Aspects, The Concept Of Personalized Medicine And A Five-year Perspective Of Dna Sequencing.

Replete with examples and mini-cases, this volulme offers cancer researchers in private, pharmacologic, and governmental institutions, biomedical statisticians, and practicing oncologists concise, thoughtfully authored guidance on the use of microarray data and analysis as clinical tools. The text carefully addresses the needs of end users researchers and physicians using microarrays as a tool to be applied in common clinical situations, and is of interest for students in medicine and biology and professionals in health care as well In this unique presentation of a revolutionary field of science, the first section introduces the domains of application for genomics and bioinformatics, investigating genetically influenced diseases, the development of new active substances, agri-food and environmental genomics. There then follows an overview of current topics central to DNA technologies, proteomics, metabolomics and bioinformatics. The whole is rounded off by a section on the ethical, legal and social aspects "Make microarray analysis an even more powerful tool. New techniques help you to get better results from your experiments. This title 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. The book is for both scientists using these techniques practically as well as those developing new analysis techniques."--Jacket Unparalleled in its scope and depth, this book brings together proteomic approaches in diagnosis and treatment from all clinical fields, including clinical toxicology. The result is a new discipline in molecular medicine that will revolutionize the treatment and prevention of cancer, stroke and other severe diseases. Authored by an international authority in the field, Cancer Diagnostics with DNA Microarrays is a complete reference work on the rapidly growing use of DNA microarray data in the diagnosis of and treatment planning for a large number of human cancers Genome research enables the establishment of the complete genetic information of organisms.