Gene Expression Data Analysis

Gene Expression Data Analysis
Author: Pankaj Barah
Publisher: CRC Press
Total Pages: 276
Release: 2021-11-08
Genre: Computers
ISBN: 1000425754

Development of high-throughput technologies in molecular biology during the last two decades has contributed to the production of tremendous amounts of data. Microarray and RNA sequencing are two such widely used high-throughput technologies for simultaneously monitoring the expression patterns of thousands of genes. Data produced from such experiments are voluminous (both in dimensionality and numbers of instances) and evolving in nature. Analysis of huge amounts of data toward the identification of interesting patterns that are relevant for a given biological question requires high-performance computational infrastructure as well as efficient machine learning algorithms. Cross-communication of ideas between biologists and computer scientists remains a big challenge. Gene Expression Data Analysis: A Statistical and Machine Learning Perspective has been written with a multidisciplinary audience in mind. The book discusses gene expression data analysis from molecular biology, machine learning, and statistical perspectives. Readers will be able to acquire both theoretical and practical knowledge of methods for identifying novel patterns of high biological significance. To measure the effectiveness of such algorithms, we discuss statistical and biological performance metrics that can be used in real life or in a simulated environment. This book discusses a large number of benchmark algorithms, tools, systems, and repositories that are commonly used in analyzing gene expression data and validating results. This book will benefit students, researchers, and practitioners in biology, medicine, and computer science by enabling them to acquire in-depth knowledge in statistical and machine-learning-based methods for analyzing gene expression data. Key Features: An introduction to the Central Dogma of molecular biology and information flow in biological systems A systematic overview of the methods for generating gene expression data Background knowledge on statistical modeling and machine learning techniques Detailed methodology of analyzing gene expression data with an example case study Clustering methods for finding co-expression patterns from microarray, bulkRNA, and scRNA data A large number of practical tools, systems, and repositories that are useful for computational biologists to create, analyze, and validate biologically relevant gene expression patterns Suitable for multidisciplinary researchers and practitioners in computer science and the biological sciences

Statistical Analysis of Gene Expression Microarray Data

Statistical Analysis of Gene Expression Microarray Data
Author: Terry Speed
Publisher: CRC Press
Total Pages: 237
Release: 2003-03-26
Genre: Mathematics
ISBN: 0203011236

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

Gene Expression Analysis

Gene Expression Analysis
Author: Nalini Raghavachari
Publisher: Humana
Total Pages: 0
Release: 2018-05-17
Genre: Medical
ISBN: 9781493978335

This volume provides experimental and bioinformatics approaches related to different aspects of gene expression analysis. Divided in three sections chapters detail wet-lab protocols, bioinformatics approaches, single-cell gene expression, highly multiplexed amplicon sequencing, multi-omics techniques, and targeted sequencing. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Gene Expression Analysis: Methods and Protocols aims provide useful information to researchers worldwide.

Microarray Gene Expression Data Analysis

Microarray Gene Expression Data Analysis
Author: Helen Causton
Publisher: John Wiley & Sons
Total Pages: 176
Release: 2009-04-01
Genre: Science
ISBN: 1444311565

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

Bioinformatics and Computational Biology Solutions Using R and Bioconductor

Bioinformatics and Computational Biology Solutions Using R and Bioconductor
Author: Robert Gentleman
Publisher: Springer Science & Business Media
Total Pages: 478
Release: 2005-12-29
Genre: Computers
ISBN: 0387293620

Full four-color book. Some of the editors created the Bioconductor project and Robert Gentleman is one of the two originators of R. All methods are illustrated with publicly available data, and a major section of the book is devoted to fully worked case studies. Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.

Molecular Pathology in Cancer Research

Molecular Pathology in Cancer Research
Author: Sunil R. Lakhani
Publisher: Springer
Total Pages: 369
Release: 2017-01-20
Genre: Medical
ISBN: 149396643X

The aim of the book is to discuss the application of molecular pathology in cancer research, and its contribution in the classification of different tumors and identification of potential molecular targets, as well as how this knowledge may be translated into clinical practice, and the huge impact this field is likely to have in the next 5 to 10 years.

Cap-Analysis Gene Expression (CAGE)

Cap-Analysis Gene Expression (CAGE)
Author: Piero Carninci
Publisher: Pan Stanford Publishing
Total Pages: 281
Release: 2010
Genre: Mathematics
ISBN: 9814241342

This book is a guide for users of new technologies, as it includes accurately proven protocols, allowing readers to prepare their samples for experiments. Although examples mainly concern mammalians, the discussion expands to other groups of eukaryotes, where these approaches are complementing genome sequencing.

Analyzing High-Dimensional Gene Expression and DNA Methylation Data with R

Analyzing High-Dimensional Gene Expression and DNA Methylation Data with R
Author: Hongmei Zhang
Publisher: CRC Press
Total Pages: 237
Release: 2020-05-14
Genre: Science
ISBN: 0429532369

Analyzing high-dimensional gene expression and DNA methylation data with R is the first practical book that shows a ``pipeline" of analytical methods with concrete examples starting from raw gene expression and DNA methylation data at the genome scale. Methods on quality control, data pre-processing, data mining, and further assessments are presented in the book, and R programs based on simulated data and real data are included. Codes with example data are all reproducible. Features: • Provides a sequence of analytical tools for genome-scale gene expression data and DNA methylation data, starting from quality control and pre-processing of raw genome-scale data. • Organized by a parallel presentation with explanation on statistical methods and corresponding R packages/functions in quality control, pre-processing, and data analyses (e.g., clustering and networks). • Includes source codes with simulated and real data to reproduce the results. Readers are expected to gain the ability to independently analyze genome-scaled expression and methylation data and detect potential biomarkers. This book is ideal for students majoring in statistics, biostatistics, and bioinformatics and researchers with an interest in high dimensional genetic and epigenetic studies.