Gohlmann / Talloen Gene Expression Studies Using Affymetrix Microarrays

Erscheinungsjahr 2010
ISBN: 978-1-4200-6516-9
Verlag: Taylor & Francis
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 359 Seiten

Reihe: Chapman & Hall/CRC Mathematical & Computational Biology

The Affymetrix GeneChip® system is one of the most widely adapted microarray platforms. However, due to the overwhelming amount of information available, many Affymetrix users tend to stick to the default analysis settings and may end up drawing sub-optimal conclusions. Written by a molecular biologist and a biostatistician with a combined decade of experience in practical expression profiling experiments and data analyses, Gene Expression Studies Using Affymetrix Microarrays tears down the omnipresent language barriers among molecular biology, bioinformatics, and biostatistics by explaining the entire process of a gene expression study from conception to conclusion.

Truly Multidisciplinary: Merges Molecular Biology, Bioinformatics, and Biostatistics
This authoritative resource covers important technical and statistical pitfalls and problems, helping not only to explain concepts outside the domain of researchers, but to provide additional guidance in their field of expertise. The book also describes technical and statistical methods conceptually with illustrative, full-color examples, enabling those inexperienced with gene expression studies to grasp the basic principles.
Gene Expression Studies Using Affymetrix Microarrays provides novices with a detailed, yet focused introductory course and practical user guide. Specialized experts will also find it useful as a translation dictionary to understand other involved disciplines or to get a broader picture of microarray gene expression studies in general. Although focusing on Affymetrix gene expression, this globally relevant guide covers topics that are equally useful for other microarray platforms and other Affymetrix applications.

Zielgruppe

Students and researchers using Affymetrix Microarrays, mathematicians, and statisticians.

Autoren/Hrsg.

Gohlmann, Hinrich

Talloen, Willem

Fachgebiete

• Naturwissenschaften Biowissenschaften Biowissenschaften DNA und Transgene Organismen

Inhaltsverzeichnis

Biological question
Why gene expression?

Biotechnological advancements

Research Question

Main types of research questions

Affymetrix microarrays

Probes
Probe sets

Array types

Standard lab processes

Affymetrix data quality

Running the experiment
Biological experiment

Microarray experiment
Data analysis preparation

Data preprocessing

Quality control

Data analysis
Why do we need statistics?

The curse of high-dimensionality

Gene filtering

Unsupervised data exploration

Detecting differential expression

Supervised prediction
Pathway analysis

Other analysis approaches

Presentation of results

Data visualization

Biological Interpretation

Data publishing

Reproducible research

Pharmaceutical R&D

The need for early indications

Critical Path Initiative

Drug Discovery

Drug Development

Clinical Trials

Using R and Bioconductor
R and Bioconductor

R and Sweave

R and Eclipse

Automated array analysis
Other software for microarray analysis

Future Perspectives
Co-analyzing different data types

The microarrays of the future

Next-gen sequencing: The end for microarrays?

Bibliography

Über Autor(innen)

Hinrich Göhlmann and Willem Talloen work at Johnson & Johnson Pharmaceutical R&D as Principal Scientist and Senior Biostatistician, respectively.