Microarray Image and Data Analysis: Theory and Practice
Since their discovery, microarrays have emerged as one of the most important biotechnological tools for studying the behavior of thousands of genes and genomic features on a genome-wide scale. The development of accurate and affordable technologies for effective and quick detection becomes paramount when considering the cost and time allowed to conduct a biological experiment. This has influenced the way in which transcriptional, proteomic and cell developmental studies are being carried out, providing a systematic way to study gene expression, elucidation of the proteome, discovering binding sites and methylation studies, all of these in a synchronized way. Transcriptional studies are one of the most important applications of microarrays, and for this, the development of gene expression arrays has helped enormously. Measuring the transcriptome or the entire repertoire of transcripts in an organism or cell lines provides a wealth of data about the relationships among DNA, transcription, translation, and phenotype. Advances in the microarray field have also allowed accurate detection that can uncover specific genetic mutations that may result in a number of human disorders. In this regard, microarrays, whether on fulllength genes or short oligonucleotide assays, constitute an efficient tool for parallel and systematic analysis.
Although different shapes, resolutions, and features of microarrays may vary substantially across platforms, techniques and applications, they can be defined in general as a small glass slide with a collection of spots or elements in which biochemical reactions take place in order to reveal quantitative information about gene or protein expression, or other biological interaction of the molecules, under specific conditions. A microarray can be conceived as a small device (Greek word “mikro” for small), in which biomolecules are arranged in a systematic manner (French word “arayer” for array). In practice, a microarray is a device that has a rectangular shape and measures a few cm long – it is typically ordered, microscopic, planar, and specific.
Microarrays have been widely used by many researchers in diverse studies in biology. To mention a few facts, there have been more than 50,000 publications pertaining to microarrays, if PubMed is used as the source of information. Extending the scope to publications on “array” would list more than 120,000 abstracts in PubMed. Various databases and resources contain a wealth of microarray data for studies of gene expression, proteomics, tissue analysis, DNA methylation, genome-wide association studies, copy number variations and aberrations, and single nucleotide polymorphism, among others. The Gene Expression Omnibus database of the National Center for Integrative Biomedical Informatics of the United States contains a wealth of gene expression data, which are publicly accessible via the Internet. These databases contain millions of samples, mostly based on microarray studies
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