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Exploration and Analysis of DNA Microarray and Other High-Dimensional Data von Amaratunga, Dhammika (eBook)

  • Erscheinungsdatum: 27.01.2014
  • Verlag: Wiley
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Exploration and Analysis of DNA Microarray and Other High-Dimensional Data

Praise for the First Edition
"...extremely well written...a comprehensive and up-to-date overview of this important field." – Journal of Environmental Quality
Exploration and Analysis of DNA Microarray and Other High-Dimensional Data, Second Edition provides comprehensive coverage of recent advancements in microarray data analysis. A cutting-edge guide, the Second Edition demonstrates various methodologies for analyzing data in biomedical research and offers an overview of the modern techniques used in microarray technology to study patterns of gene activity. The new edition answers the need for an efficient outline of all phases of this revolutionary analytical technique, from preprocessing to the analysis stage. Utilizing research and experience from highly-qualified authors in fields of data analysis, Exploration and Analysis of DNA Microarray and Other High-Dimensional Data, Second Edition features: A new chapter on the interpretation of findings that includes a discussion of signatures and material on gene set analysis, including network analysis
New topics of coverage including ABC clustering, biclustering, partial least squares, penalized methods, ensemble methods, and enriched ensemble methods
Updated exercises to deepen knowledge of the presented material and provide readers with resources for further study
The book is an ideal reference for scientists in biomedical and genomics research fields who analyze DNA microarrays and protein array data, as well as statisticians and bioinformatics practitioners. Exploration and Analysis of DNA Microarray and Other High-Dimensional Data, Second Edition is also a useful text for graduate-level courses on statistics, computational biology, and bioinformatics.

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Exploration and Analysis of DNA Microarray and Other High-Dimensional Data

Chapter 2
Genomics Basics
It is useful to review the basic concepts of modern molecular biology before fully immersing ourselves in the world of microarrays. We are sure that readers who have had limited exposure to this fast-developing field would appreciate this review, others may skip ahead. Genomics is a fascinating subject; after all, it is the story of life, and can occupy a multivolume book just by itself. In the interest of space, of course, it is necessary that we confine our discussion to those topics that are essential to an understanding of the science underlying microarrays, leaving other topics for interested readers to explore on their own. Some excellent general references that we, not being trained as molecular biologists ourselves, have found useful are listed at the end of the chapter.
2.1 Genes
From ancient times, it was suspected that there existed some sort of a hereditary mechanism that carried information from parent to child. It is because of this mechanism that family members tend to exhibit similar characteristics or traits . For example, they tend to resemble each other in terms of appearance and physical characteristics such as skin color; they tend to be predisposed toward certain diseases such as diabetes, cancer, and heart disease; and so on. However, inheritance is clearly not a perfect copying process. For example, a child of brown-eyed parents could turn out to be blue-eyed. Despite the efforts over the years of many leading scientists and thinkers to understand the hereditary mechanism, its precise nature remained an intriguing mystery until quite recently.
Following centuries of speculation and research, the existence of discrete hereditary units, which we now call genes , has been firmly established. Each gene, either by itself or in combination with some other genes, provides a clear and unambiguous set of instructions for producing some property of its organism. The complete set of genes in an organism, essentially the master blueprint for that organism, is referred to as its genome . This blueprint contains all the hereditary instructions for building, operating, and maintaining the organism, and for passing life in like form on to the next generation of that organism.
Until the twentieth century, there was hardly any concrete information as to what genes were and how they operated. Then, a panoply of innovative research work and pathbreaking discoveries over (roughly) the first half of the twentieth century gave genes a chemical (molecular) existence. This culminated in the pivotal realization that genes are made of deoxyribonucleic acid (DNA).
2.2 Deoxyribonucleic Acid
A DNA molecule consists of two long strands wound tightly around each other in a spiral structure known as a double helix . The structure has been likened to a twisted ladder, whose sides are made of sugar and phosphate and whose rungs are made of bases.
Each strand of the DNA molecule (i.e., each side of the ladder once it has been untwisted and straightened out) is a linear arrangement of repeating similar units called nucleotides . Every nucleotide has three components: a sugar (deoxyribose), a phosphate group, and a nitrogenous base. The base is one of adenine (A), thymine (T), guanine (G), or cytosine (C). The bases on one strand are paired with the bases on the other strand according to the complementary base pairing rules (also called the Watson - Crick base pairing rules ): adenine only pairs with thymine, guanine only pairs with cytosine. The pairs so formed are called base pairs (bp); they form the coplanar rungs of the ladder. The force that holds a bp together is a weak hydrogen bond. Even though each individual bond is weak, their cumulative effect along the strands is strong enough to bind the two strands tightly together. A

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