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DNA Microarray Analysis

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Reproductive Endocrinology

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The methods described in Chapter 9 are designed to look at the expression of specific selected genes in relatively small numbers. To ascertain mRNA changes that occur on a much larger scale microarray analyses can be performed. A microarray, also known as biochip by analogy with the computer industry terminology, can be described as the sum of a multitude of similar miniaturized assays that take place simultaneously on a small surface. Microarrays types include those for DNA, tissue, protein, and bacteria. DNA microarrays include those covering the whole genome, intergenic regions, and the coding regions of genes. Within this chapter we will focus on DNA microarrays with emphasis on arrays for analyzing gene expression.

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Authors and Affiliations

  1. Department of Pediatrics, University of Maryland at Baltimore School of Medicine, Baltimore, MD, USA

    Gheorghe T. Braileanu

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  1. Gheorghe T. Braileanu
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Correspondence to Gheorghe T. Braileanu .

Editor information

Editors and Affiliations

     

    Fluxomics:

    identification of the dynamic changes of molecules within a cell over time.

    Genomics:

    the analysis of gene expression and regulation in cell, tissue or organs under given conditions [2,47] including how the genes interact with each other and with the environment. It has the potential to revolutionize the practice of medicine.

    Glycomics:

    identification of all carbohydrates in a cell or tissues.

    Glycoproteomics:

    a branch of proteomics that identifies, catalogs, and characterizes glycoproteins.

    Interactomics:

    identification of protein–protein interactions but also include interactions between all molecules within a cell.

    Metabolomics:

    identification and measurement of all small metabolites in a cell or tissue.

    Pharmacogenomics:

    the combination of pharmacology and genomics that deals with analysis of the genome and its products (RNA and proteins) related to drug responses.

    Phosphoproteomics:

    a branch of proteomics that identifies, catalogs, and characterizes phosphorylated proteins.

    Piezoelectricity:

    the ability of some materials mainly crystals and certain ceramics to generate an electric charge in response to a mechanical stress. If the material is not shortcircuited, the applied charge induces a voltage across the material.

    Protein microarray:

    a substrate of glass or silicon on which different molecules of protein have been affixed at separate locations in an ordered manner thus forming a microscopic array. These are used to identify protein–protein interactions, substrates of protein kinases, or the targets of biologically active small molecules. The main use of the protein microarrays, also termed protein chip, is to determine the presence and/or the amount of proteins in biological samples, e.g. blood. One common protein microarray is the antibody microarray, where antibodies (most frequently monoclonal) are spotted onto the protein chip and are used as capture-molecules to detect proteins from cell lysates. There are several types of protein chips; however, the most common are glass slide chips and nano-well arrays.

    Proteomics:

    complete identification of proteins and protein expression patterns of a cell or tissue through two-dimensional gel electrophoresis or other multi-dimensional protein separation techniques and mass spectrometry. It is a large-scale study of proteins, particularly of their structure and function under given conditions [2]. This term was created to make an analogy with genomics [47]. Proteomics is much more complicated than genomics: while the genome is a rather constant entity, the proteome differs from cell to cell and is constantly changing through its biochemical interactions with the genome and the environment. One organism has radically different protein expression in different parts of its body, during different stages of its life cycle and under different environmental conditions [47].

    SAGE:

    Serial Analysis of Gene Expression.

    System biology:

    the strategy of pursuing integration of complex data about biological interactions from diverse experimental sources using interdisciplinary tools and high-throughput experiments and bioinformatics.

    Transcriptomic:

    measurement of gene expression in whole cells or tissue by DNA microarray or SAGE.

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    Braileanu, G.T. (2009). DNA Microarray Analysis. In: Chedrese, P. (eds) Reproductive Endocrinology. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-88186-7_10

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    • DOI: https://doi.org/10.1007/978-0-387-88186-7_10

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    • Publisher Name: Springer, Boston, MA

    • Print ISBN: 978-0-387-88185-0

    • Online ISBN: 978-0-387-88186-7

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