Microarray Gene Expression Data Analysis: A Beginner's Guide

Book Description

Microarray technology is arguably the most important recent breakthrough in molecular biology. It enables researchers to obtain snapshots of gene expression for all the genes in a genome in a single experiment. Microarray experiments generate massive amounts of data that can be analysed to extract new knowledge about the underlying biological processes.This guide covers aspects of designing microarray experiments and analysing the data generated, and includes 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.

Customer Reviews:

A good introduction to the topic .......2007-05-20

Microarrays are a tool for monitoring gene expression levels for thousands of genes in parallel. This technology is very useful since patterns in the gene expression can be used for molecular characterization of phenomena that range from disease states and response to stimuli to the differences between cells of different types. The amount of information obtained from one microarray experiment can be large. These large amounts of information present new challenges in the areas of data storage, management, and analysis by biologists who are not accustomed to dealing with this much data. Also, the software used for data analysis is usually written by mathematicians and statisticians that have a minimum of training in biology.

This book addresses some of the issues faced by researchers who are beginning their first microarray experiments. It covers various aspects of designing and analyzing the results of microarray experiments. Microarrays are not limited to the study of gene expression, but this remains the most common use of the technology and therefore is the only use of arrays discussed here. This book attempts to explain the underlying concepts and principles routinely used in analysis of gene expression data. The book should be accessible by statisticians, computer scientists, and students of bioinformatics who want a grounding in the types of analysis currently used to study microarray data.

The book begins with an introductory chapter which is followed by three major chapters. As with any technology that has the capacity to detect small changes in a highly dynamic system, the underlying experimental design and the manner in which an experiment is conducted is critical for obtaining high quality data. Chapter two addresses these issues. The raw data from microarray experiments are images that must be transformed and organized into gene expression matrices. These transformations are the subject of chapter 3. Finally, in chapter 4, the common methods used for analyzing gene expression data matrices with the goal of obtaining new insights into biology are discussed. The book does a pretty good job of providing the reader with a general understanding of the nature of microarray data and how it can be analyzed. It was never meant to be a reference book or a comprehensive review, just a gentle introduction.

Well written, short explanations but nevertheless understandable.......2005-07-06

Certainly, this book can not give a complete description of microarrays, neither from an experimental nor a theoretical side. Nevertheless, the issues presented and discussed provide the reader with a solid basis for more advanced studies.

In my opinion, this book is well written, the explanations given are descriptive and understandable and its overall organization is plausible. I recommend this book as an introduction for the analysis of microarray data, because it provides a good overview of existing methods in this field. A warning: This does not mean, that all these methods are thorougly expained! It just provides an overview!! If you want to learn, e.g., clustering methods, you should consult another book (probably no other book about microarrays but a decent book dealing only with data analysis in general or clustering methods...)

Pcr Protocols: A GUIDE TO MTHODS & APPLICATIONS

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Pcr Protocols: A GUIDE TO MTHODS & APPLICATIONS
MICHAEL INNIS
Manufacturer: Academic Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 0123721806

Book Description

The correct procedures you need for frustration-free PCR methods and applications are contained in this complete, step-by-step, clearly written, inexpensive manual.

Key Features
* This first-rate guide will help you
* Avoid contamination--with specific instructions on setting up your lab
* Avoid cumbersome molecular biological techniques
* Discover new applications
* Simply call our toll-free, 800 number listed below or cut out the coupon, fill in the blanks, and mail it to us with your check, credit-card number, or money order; We'll send you the book and you'll get your answers

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Best PCR manual there is!

PCR Primer: A Lab Manual
Carl W., Ed. Dieffenbach
Manufacturer: Cold Spring Harbor Laboratory Press
ProductGroup: Book
Binding: Paperback

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ASIN: 0879696540

Book Description

From its first-published account in 1985, the polymerase chain reaction has become a standard research tool in a wide range of laboratories. Its impact has been felt in basic molecular biological research, clinical research, forensics, evolutionary studies, and the Human Genome Project. The PCR technique originally conceived by Nobel laureate Kary Mullis has proven to be exceptionally adaptable and has been transformed into a myriad array of methods, each with different applications.

PCR Primer: A Laboratory Manual introduces the complex world of PCR by beginning at an accessible level and then moving to more advanced levels of application. First, the practical requirements for performing PCR and other amplification techniques in the lab are introduced and then the basic aspects of the technique are explained by exploring important issues such as sample preparation, primer design, efficiency, detection of products, and quantitation. Protocols for a wide range of PCR and amplification techniques—each written by an expert investigator—are presented for cloning, sequencing, mutagenesis, footprinting, library construction and screening, exon trapping, differential display, and expression, and these include RT-PCR, RNA PCR, LCR, multiplex PCR, panhandle PCR, capture PCR, expression PCR, 3' and 5' RACE, immune PCR, in situ PCR, and ligation-mediated PCR. Each protocol is augmented by analysis and troubleshooting sections and complete references.

Customer Reviews:

Best PCR manual there is!.......2000-09-20

I have used two different protocols from this book, 1, RACE-PCR and 2, mutagenesis.These two methods were described very well, both theoretically and practically. The protocols were described in detail, were easy to follow, and they work! I'm sure that the other protocols in this book also work equally well. If you do PCR, you need this book!

DNA Science: A First Course, Second Edition

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My High School Textbook
Not Bad
Great Intro to Genetic Science
spotless

DNA Science: A First Course, Second Edition
David A. Micklos
Manufacturer: Cold Springs Harbor Laboratory Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 0879696362

Book Description

This is the second edition of a highly successful textbook (over 50,000 copies sold) in which a highly illustrated, narrative text is combined with easy-to-use thoroughly reliable laboratory protocols. It contains a fully up-to-date collection of 12 rigorously tested and reliable lab experiments in molecular biology, developed at the internationally renowned Dolan DNA Learning Center of Cold Spring Harbor Laboratory, which culminate in the construction and cloning of a recombinant DNA molecule.

Proven through more than 10 years' of teaching at research and nonresearch colleges and universities, junior colleges, community colleges, and advanced biology programs in high school, this book has been successfully integrated into introductory biology, general biology, genetics, microbiology, cell biology, molecular genetics, and molecular biology courses.

The first eight chapters have been completely revised, extensively rewritten, and updated. The new coverage extends to the completion of the draft sequence of the human genome and the enormous impact these and other sequence data are having on medicine, research, and our view of human evolution. All sections on the concepts and techniques of molecular biology have been updated to reflect the current state of laboratory research.

The laboratory experiments cover basic techniques of gene isolation and analysis, honed by over 10 years of classroom use to be thoroughly reliable, even in the hands of teachers and students with no prior experience. Extensive prelab notes at the beginning of each experiment explain how to schedule and prepare, while flow charts and icons make the protocols easy to follow.

As in the first edition of this book, the laboratory course is completely supported by quality-assured products from the Carolina Biological Supply Company, from bulk reagents, to useable reagent systems, to single-use kits, thus satisfying a broad range of teaching applications.

Customer Reviews:

My High School Textbook.......2007-07-04

This was used for my high school semester course "DNA Sci part 1" textbook used with Watson's Recombinant DNA textbook. DNA Science:A 1st Course, 2nd edi was useful in supplementing the updates in recent genetic advances and some newer, better graphic representations. I found this to be an easy textbook to read, although not intended for those without a biology and chemistry background since the book does not waste much ink on describing what should have already been learned. The other students in my class seemed to find this book to be a clear, understandable textbook as well.

A very good first course textbook that keeps a student (or any person) interested. Nice big, clear print as well. The laboratories were the standard same as in the Recombinant DNA textbook.

Not Bad.......2005-08-03

I havent read much of this yet, we really wont be using much until the second quarter but so far it seems not bad i hope this review is as helpful to you as it would have been for me oh yeah dna is interesting

Great Intro to Genetic Science.......2005-07-28

This is the best single source of information on Genetic Science I have run across. Comprehensive from history, to theory, to lab practice. Highly recommended! Great illustrations and very clearly written. Its targeted to people with a serious interest in the field, definitely not for the "Genetic Science for Dummies" crowd.

spotless.......2004-03-21

This book is the best book on the subject on the market. The subject matter is juxtaposed by easy yet informative experiments that can be carried out in a normal scholastic setting. I hear the writers are all hotties.

Molecular Cloning: A Laboratory Manual (3-Volume Set)

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Molecular Cloning: A Laboratory Manual (3-Volume Set)
a formerly essential classic
the BIBLE of every biologist
the BIBLE of every biologist
Excellent reference for all

Molecular Cloning: A Laboratory Manual (3-Volume Set)
Joe Sambrook
Manufacturer: COLD SPRING HARBOR LABORATORY PRESS
ProductGroup: Book
Binding: Hardcover

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ASIN: 0879695765

Book Description

The first two editions of this manual have been mainstays of molecular biology for nearly twenty years, with an unrivalled reputation for reliability, accuracy, and clarity.

In this new edition, authors Joe Sambrook and David Russell have completely updated the book, revising every protocol and adding a mass of new material, to broaden its scope and maintain its unbeatable value for studies in genetics, molecular cell biology, developmental biology, microbiology, neuroscience, and immunology.

Handsomely redesigned and presented in new bindings of proven durability, this three-volume work is essential for everyone using today's biomolecular techniques.

The opening chapters describe essential techniques, some well-established, some new, that are used every day in the best laboratories for isolating, analyzing and cloning DNA molecules, both large and small.

These are followed by chapters on cDNA cloning and exon trapping, amplification of DNA, generation and use of nucleic acid probes, mutagenesis, and DNA sequencing.

The concluding chapters deal with methods to screen expression libraries, express cloned genes in both prokaryotes and eukaryotic cells, analyze transcripts and proteins, and detect protein-protein interactions.

The Appendix is a compendium of reagents, vectors, media, technical suppliers, kits, electronic resources and other essential information.

As in earlier editions, this is the only manual that explains how to achieve success in cloning and provides a wealth of information about why techniques work, how they were first developed, and how they have evolved.

Customer Reviews:

Molecular Cloning: A Laboratory Manual (3-Volume Set).......2007-03-19

This revised version of the Standard Lab Handbook has been improved, completed with new techniques and search is facilitated by the indices added at the end of each volume.

a formerly essential classic.......2005-11-24

For many years the previous edition of this set was an essential reference in molecular biology labs. At present however, there are too many good protocol books out there to really make this argument. The book is pretty strong in explaining theory, and answering the question of why certain procedures are either necessary, useful, or worthless, however it is not as practical as many other books, such as Short Protocols. Still a good reference overall, but no longer stands alone, and I recommend checking out as much of the competition as possible before deciding whether to make the investment in it.

the BIBLE of every biologist.......2003-01-31

So few and so much to say about this bible of Biology at the bench...
You'll really find everything you want in it, including the composition of all the buffers and solutions, the new protocols for high-tech biology (FLIM-FRET), some paragraphs about bioinformatics and more.Incredibly precise, this book is consequently a big book (3 huge volumes), so better know exactly wath you're looking for before opening it!
The must have of every lab!

the BIBLE of every biologist.......2003-01-31

Excellent reference for all.......2002-03-09

In this 3 volume set of books the authors summarize the most important laboratory protocols for DNA analysis and cloning. As someone involved in computational biology and mathematical gene sequence analysis, I was needing such a summary to get an idea of just how genetic engineering is actually practiced in the laboratory. The book is definitely written for those readers that are very experienced in these "wet" techniques, but it still could be perused profitably by anyone who is curious about genetic engineering. There is also an excellent website that owners of the books can go to and search for protocols and obtain updates and additions to the protocols.

At the beginning of each chapter, the authors give an introduction to the protocols and this is of an enormous help to those readers with only rudimentary acquaintance with the laboratory procedures. Typically, this introduction contains an historical summary of the procedures as they were developed or discovered. One can only marvel at the ingenuity of the discoverers of these techniques. These introductions are fairly straightforward to read, even for those that are not experts in biochemistry.

At the end of each chapter, the authors include an "information panel" that gives a more in-depth view of the biochemistry or genetics behind the procedures. These are summaries and are highly specialized, and are again meant for experienced readers. A very lengthy list of references is also included at the end of each chapter.

Book Description

This manual encompasses an integrated series of molecular biology laboratory exercises that involve the cloning and analysis of the bioluminescence (lux) genes from the marine bacterium Vibrio fischeri. The manual is divided into discrete units with each demonstrating one or more aspects of the cloning project. The manual is based on one of nature's most fascinating biological phenomenon: the biological production of light. This results in a recurrent theme of interest and makes the project very relevant to interdisciplinary topics such as fish symbiosis, biochemistry, biophysics, etc. Includes instruction in the basic techniques of modern molecular biology: DNA isolation and analysis, DNA restriction, agarose gel electrophoresis, ligations, transformation of recombinant DNA, preparation and screening a genomic library, restriction mapping, Southern blotting, hybridization, DNA sequencing, pulsed field gel electrophoresis. Designed for a one semester course in Molecular Biology. Also appropriate for a molecular biology component of Microbial Genetics, Genetics, Biochemistry, or Advanced Microbiology courses.

Customer Reviews:

This book badly needs revision.......2002-03-20

The material in the introductory text preceeding most of the exercizes lacks clarity, is poorly written and sadly confuses the reader. The introduction to the lux operon seems to be a very good example to illustrate the point. This book was made possible by a grant from the NSF and if the authors continue to market this book without revision it would be just be a travesty and an insult to intelligence. Please take note of the shortcomings of this book before decinding to buy it.

Two thumbs up.......2002-03-14

One of the best lab texts around. Provides a thorough exposure to the most commonly used molecular laboratory techniques. Highly recommended for faculty, who focus on creating a hands-on learning environment.

Wonderful Lab Manual.......2001-02-27

This is a wonderful text clear and concise, it explores the bulk of the basic lab techniques and procedures in molecular biology. This highly readable text builds on the cumulative experiences of some highly skilled academicians and researchers. Highly recommended for any molecular biology lab course or as a useful reference.

Apoptosis Methods and Protocols (Methods in Molecular Biology (Cloth))

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Apoptosis Methods and Protocols (Methods in Molecular Biology (Cloth))
Hugh, Ed. Brady
Manufacturer: Humana Press
ProductGroup: Book
Binding: Hardcover

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When Cells Die II: A Comprehensive Evaluation of Apoptosis and Programmed Cell Death

ASIN: 0896038734

Book Description

A collection of cutting-edge techniques for detecting and quantifying apoptosis, understanding its biochemistry, and for identifying the genes and proteins that regulate and carry it out. Described in step-by-step detail, these readily reproducible methods range from flow cytometry and immunohistochemical procedures to kinase activity assays, yeast two-hybrid screening, and the cloning of novel genes by differential expression. The protocols follow the successful Methods in Molecular Biologyâ„¢ series format, each one offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of equipment and reagents, and tips on troubleshooting and avoiding known pitfalls. Apoptosis Methods and Protocols constitutes a key technical reference to the significant methodologies used in the field, as well as offering novice and experienced researchers alike powerful tools to illuminate the phenomenon of programmed cell death.

Gene Transfer: Delivery And Expression of DNA And RNA, A Laboratory Manual

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The State of the Art as of Late 2006

Gene Transfer: Delivery And Expression of DNA And RNA, A Laboratory Manual
Theodore, Ed. Friedman
Manufacturer: Cold Spring Harbor Laboratory Press
ProductGroup: Book
Binding: Paperback

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ASIN: 0879697652
Release Date: 2006-12-01

Customer Reviews:

The State of the Art as of Late 2006.......2007-03-07

This book describes a series of protocols that offer ways to deliver genes into mammalian cells. About half the book describes viral techniques where a virus is used to do the transport and delivery. The other half describes non-viral methods. The book has some 75 different techniques, each described by a researcher who has been using/developing that method.

Note that many of these techniques are brand new and still in the stage of being developed. Some of them are likely to prove useful, others will be of limited use, perhaps in a niche application or will simply lead to better techniques later on.

Dr. Rossi (Bechmann Research Institute) and Dr. Friedmann (UCSD) serve as editors of the book. It is called a Laboratory Manual as the protocols are presented in a stepwise, 'cookbook' style.

The book was published in early 2007 and should be considered an accurate reflection of the state of the art as of late in 2006.

Nuclease Methods and Protocols (Methods in Molecular Biology (Cloth))

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Nuclease Methods and Protocols (Methods in Molecular Biology (Cloth))
Catherine H., Ed. Schein
Manufacturer: Humana Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 0896036790

Book Description

Scientists at the forefront of academic research and pharmaceutical drug development offer their well-polished methodologies for protein nucleases that can be used to determine their activity, structure, interaction with other molecules, and physiological role. Protocols range from methods for characterizing nucleases, to correlating nuclease structure and function, to the use of nucleases in cloning. Recombinant techniques for expressing and isolating nucleases are covered, as well as methods specific for dealing with protein/nucleic acid complexes. Each chapter contains a minireview of a specific nuclease or nuclease-related theme, a discussion of why and when to use the assay in question, and an explanation of the thinking that went into its development. Comprehensive and highly practical, Nuclease Methods and Protocols offers both novice and experienced researchers a deeper understanding of their importance in cell metabolism, growth control mechanisms, and, increasingly, in diagnostics and therapeutics.

Directed Enzyme Evolution: Screening and Selection Methods (Methods in Molecular Biology (Cloth))

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Directed Enzyme Evolution: Screening and Selection Methods (Methods in Molecular Biology (Cloth))
Frances H., Ed. Arnold
Manufacturer: Humana Press
ProductGroup: Book
Binding: Hardcover

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Directed Evolution Library Creation: Methods and Protocols (Methods in Molecular Biology (Cloth))

ASIN: 158829286X

Book Description

Seasoned practitioners from many leading laboratories describe their best readily reproducible screening strategies for isolating useful clones. These techniques have been optimized for sensitivity, high throughput, and robustness, and are of proven utility for directed evolution purposes. The assays presented use a variety of techniques, including genetic complementation, microtiter plates, solid-phase screens with colorimetric substrates, and flow cytometric screens. An accompanying volume, Directed Evolution Library Creation: Methods and Protocols (ISBN 1-58829-285-1), describes readily reproducible methods for the creation of mutated DNA molecules and DNA libraries.

Copy for Both Volumes

Directed Evolution Library Creation: Methods and Protocols and Directed Enzyme Evolution: Screening and Selection Methods constitute an extraordinary collection of all the key methods used today for directed evolution research. Described in step-by-step detail to ensure robust experimental results, these methods will enable both newcomers and more experienced investigators to design and implement directed evolution strategies for the engineering of novel proteins. The first volume describes methods for the creation of mutated DNA molecules, or DNA libraries, encoding variants of desired proteins. The second volume describes methods for screening DNA libraries to isolate mutant proteins that exhibit a specified function.

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