In the past several years, DNA microarray technology has attracted tremendous interest in both the scientific community and in industry. With its ability to simultaneously measure the activity and interactions of thousands of genes, this modern technology promises unprecedented new insights into mechanisms of living systems. Currently, the primary applications of microarrays include gene discovery, disease diagnosis and prognosis, drug discovery (pharmacogenomics), and toxicological research (toxicogenomics). Typical scientific tasks addressed by microarray experiments include the identification of coexpressed genes, discovery of sample or gene groups with similar expression patterns, identification of genes whose expression patterns are highly differentiating with respect to a set of discerned biological entities (e.g., tumor types), and the study of gene activity patterns under various stress conditions (e.g., chemical treatment). More recently, the discovery, modeling, and simulation of regulatory gene networks, and the mapping of expression data to metabolic pathways and chromosome locations have been added to the list of scientific tasks that are being tackled by microarray technology. Each scientific task corresponds to one or more so-called data analysis tasks. Different types of scientific questions require different sets of data analytical techniques. Broadly speaking, there are two classes of elementary data analysis tasks, predictive modeling and pattern-detection. Predictive modeling tasks are concerned with learning a classification or estimation function, whereas pattern-detection methods screen the available data for interesting, previously unknown regularities or relationships.

As natural phenomena are being probed and mapped in ever-greater detail, scientists in genomics and proteomics are facing an exponentially growing vol­ ume of increasingly complex-structured data, information, and knowledge. Ex­ amples include data from microarray gene expression experiments, bead-based and microfluidic technologies, and advanced high-throughput mass spectrom­ etry. A fundamental challenge for life scientists is to explore, analyze, and interpret this information effectively and efficiently. To address this challenge, traditional statistical methods are being complemented by methods from data mining, machine learning and artificial intelligence, visualization techniques, and emerging technologies such as Web services and grid computing. There exists a broad consensus that sophisticated methods and tools from statistics and data mining are required to address the growing data analysis and interpretation needs in the life sciences. However, there is also a great deal of confusion about the arsenal of available techniques and how these should be used to solve concrete analysis problems. Partly this confusion is due to a lack of mutual understanding caused by the different concepts, languages, methodologies, and practices prevailing within the different disciplines.

As natural phenomena are being probed and mapped in ever-greater detail, scientists in genomics and proteomics are facing an exponentially growing vol­ ume of increasingly complex-structured data, information, and knowledge. Ex­ amples include data from microarray gene expression experiments, bead-based and microfluidic technologies, and advanced high-throughput mass spectrom­ etry. A fundamental challenge for life scientists is to explore, analyze, and interpret this information effectively and efficiently. To address this challenge, traditional statistical methods are being complemented by methods from data mining, machine learning and artificial intelligence, visualization techniques, and emerging technologies such as Web services and grid computing. There exists a broad consensus that sophisticated methods and tools from statistics and data mining are required to address the growing data analysis and interpretation needs in the life sciences. However, there is also a great deal of confusion about the arsenal of available techniques and how these should be used to solve concrete analysis problems. Partly this confusion is due to a lack of mutual understanding caused by the different concepts, languages, methodologies, and practices prevailing within the different disciplines.

In the past several years, DNA microarray technology has attracted tremendous interest in both the scientific community and in industry. With its ability to simultaneously measure the activity and interactions of thousands of genes, this modern technology promises unprecedented new insights into mechanisms of living systems. Currently, the primary applications of microarrays include gene discovery, disease diagnosis and prognosis, drug discovery (pharmacogenomics), and toxicological research (toxicogenomics). Typical scientific tasks addressed by microarray experiments include the identification of coexpressed genes, discovery of sample or gene groups with similar expression patterns, identification of genes whose expression patterns are highly differentiating with respect to a set of discerned biological entities (e.g., tumor types), and the study of gene activity patterns under various stress conditions (e.g., chemical treatment). More recently, the discovery, modeling, and simulation of regulatory gene networks, and the mapping of expression data to metabolic pathways and chromosome locations have been added to the list of scientific tasks that are being tackled by microarray technology. Each scientific task corresponds to one or more so-called data analysis tasks. Different types of scientific questions require different sets of data analytical techniques. Broadly speaking, there are two classes of elementary data analysis tasks, predictive modeling and pattern-detection. Predictive modeling tasks are concerned with learning a classification or estimation function, whereas pattern-detection methods screen the available data for interesting, previously unknown regularities or relationships.

The book addresses the requirement of scientists and researchers to gain a basic understanding of microarray analysis methodologies and tools. It is intended for students, teachers, researchers, and research managers who want to understand the state of the art and of the presented methodologies and the areas in which gaps in our knowledge demand further research and development. The book is designed to be used by the practicing professional tasked with the design and analysis of microarray experiments or as a text for a senior undergraduate- or graduate level course in analytical genetics, biology, bioinformatics, computational biology, statistics and data mining, or applied computer science.

As natural phenomena are being probed and mapped in ever-greater detail, scientists in genomics and proteomics are facing an exponentially growing vol­ ume of increasingly complex-structured data, information, and knowledge. Ex­ amples include data from microarray gene expression experiments, bead-based and microfluidic technologies, and advanced high-throughput mass spectrom­ etry. A fundamental challenge for life scientists is to explore, analyze, and interpret this information effectively and efficiently. To address this challenge, traditional statistical methods are being complemented by methods from data mining, machine learning and artificial intelligence, visualization techniques, and emerging technologies such as Web services and grid computing. There exists a broad consensus that sophisticated methods and tools from statistics and data mining are required to address the growing data analysis and interpretation needs in the life sciences. However, there is also a great deal of confusion about the arsenal of available techniques and how these should be used to solve concrete analysis problems. Partly this confusion is due to a lack of mutual understanding caused by the different concepts, languages, methodologies, and practices prevailing within the different disciplines.

In the past several years, DNA microarray technology has attracted tremendous interest in both the scientific community and in industry. With its ability to simultaneously measure the activity and interactions of thousands of genes, this modern technology promises unprecedented new insights into mechanisms of living systems. Currently, the primary applications of microarrays include gene discovery, disease diagnosis and prognosis, drug discovery (pharmacogenomics), and toxicological research (toxicogenomics). Typical scientific tasks addressed by microarray experiments include the identification of coexpressed genes, discovery of sample or gene groups with similar expression patterns, identification of genes whose expression patterns are highly differentiating with respect to a set of discerned biological entities (e.g., tumor types), and the study of gene activity patterns under various stress conditions (e.g., chemical treatment). More recently, the discovery, modeling, and simulation of regulatory gene networks, and the mapping of expression data to metabolic pathways and chromosome locations have been added to the list of scientific tasks that are being tackled by microarray technology. Each scientific task corresponds to one or more so-called data analysis tasks. Different types of scientific questions require different sets of data analytical techniques. Broadly speaking, there are two classes of elementary data analysis tasks, predictive modeling and pattern-detection. Predictive modeling tasks are concerned with learning a classification or estimation function, whereas pattern-detection methods screen the available data for interesting, previously unknown regularities or relationships.

As natural phenomena are being probed and mapped in ever-greater detail, scientists in genomics and proteomics are facing an exponentially growing vol­ ume of increasingly complex-structured data, information, and knowledge. Ex­ amples include data from microarray gene expression experiments, bead-based and microfluidic technologies, and advanced high-throughput mass spectrom­ etry. A fundamental challenge for life scientists is to explore, analyze, and interpret this information effectively and efficiently. To address this challenge, traditional statistical methods are being complemented by methods from data mining, machine learning and artificial intelligence, visualization techniques, and emerging technologies such as Web services and grid computing. There exists a broad consensus that sophisticated methods and tools from statistics and data mining are required to address the growing data analysis and interpretation needs in the life sciences. However, there is also a great deal of confusion about the arsenal of available techniques and how these should be used to solve concrete analysis problems. Partly this confusion is due to a lack of mutual understanding caused by the different concepts, languages, methodologies, and practices prevailing within the different disciplines.

As natural phenomena are being probed and mapped in ever-greater detail, scientists in genomics and proteomics are facing an exponentially growing vol­ ume of increasingly complex-structured data, information, and knowledge. Ex­ amples include data from microarray gene expression experiments, bead-based and microfluidic technologies, and advanced high-throughput mass spectrom­ etry. A fundamental challenge for life scientists is to explore, analyze, and interpret this information effectively and efficiently. To address this challenge, traditional statistical methods are being complemented by methods from data mining, machine learning and artificial intelligence, visualization techniques, and emerging technologies such as Web services and grid computing. There exists a broad consensus that sophisticated methods and tools from statistics and data mining are required to address the growing data analysis and interpretation needs in the life sciences. However, there is also a great deal of confusion about the arsenal of available techniques and how these should be used to solve concrete analysis problems. Partly this confusion is due to a lack of mutual understanding caused by the different concepts, languages, methodologies, and practices prevailing within the different disciplines.

In the past several years, DNA microarray technology has attracted tremendous interest in both the scientific community and in industry. With its ability to simultaneously measure the activity and interactions of thousands of genes, this modern technology promises unprecedented new insights into mechanisms of living systems. Currently, the primary applications of microarrays include gene discovery, disease diagnosis and prognosis, drug discovery (pharmacogenomics), and toxicological research (toxicogenomics). Typical scientific tasks addressed by microarray experiments include the identification of coexpressed genes, discovery of sample or gene groups with similar expression patterns, identification of genes whose expression patterns are highly differentiating with respect to a set of discerned biological entities (e.g., tumor types), and the study of gene activity patterns under various stress conditions (e.g., chemical treatment). More recently, the discovery, modeling, and simulation of regulatory gene networks, and the mapping of expression data to metabolic pathways and chromosome locations have been added to the list of scientific tasks that are being tackled by microarray technology. Each scientific task corresponds to one or more so-called data analysis tasks. Different types of scientific questions require different sets of data analytical techniques. Broadly speaking, there are two classes of elementary data analysis tasks, predictive modeling and pattern-detection. Predictive modeling tasks are concerned with learning a classification or estimation function, whereas pattern-detection methods screen the available data for interesting, previously unknown regularities or relationships.

The book addresses the requirement of scientists and researchers to gain a basic understanding of microarray analysis methodologies and tools. It is intended for students, teachers, researchers, and research managers who want to understand the state of the art and of the presented methodologies and the areas in which gaps in our knowledge demand further research and development. The book is designed to be used by the practicing professional tasked with the design and analysis of microarray experiments or as a text for a senior undergraduate- or graduate level course in analytical genetics, biology, bioinformatics, computational biology, statistics and data mining, or applied computer science.

As natural phenomena are being probed and mapped in ever-greater detail, scientists in genomics and proteomics are facing an exponentially growing vol­ ume of increasingly complex-structured data, information, and knowledge. Ex­ amples include data from microarray gene expression experiments, bead-based and microfluidic technologies, and advanced high-throughput mass spectrom­ etry. A fundamental challenge for life scientists is to explore, analyze, and interpret this information effectively and efficiently. To address this challenge, traditional statistical methods are being complemented by methods from data mining, machine learning and artificial intelligence, visualization techniques, and emerging technologies such as Web services and grid computing. There exists a broad consensus that sophisticated methods and tools from statistics and data mining are required to address the growing data analysis and interpretation needs in the life sciences. However, there is also a great deal of confusion about the arsenal of available techniques and how these should be used to solve concrete analysis problems. Partly this confusion is due to a lack of mutual understanding caused by the different concepts, languages, methodologies, and practices prevailing within the different disciplines.