What Is an Array

As Fig. 8.1 shows, an expression array is simply a list of values representing the amounts of each mRNA species found in a sample. This concept greatly simplifies the usual red-green display and points out that "arrays" are a simple list of RNA quantities resulting from any measurement technique. Tab. 8.1 shows six different RNA detection methods used to quantify large sets of RNA expression values.

Finally, although not usually thought of as an "array", methods derived from RNA-based representational difference analysis (RNA-RDA) subtraction suppression hybridization (SSH) [1], use selective forms of PCR to eliminate those sequences found in common between two cDNA collections [2].

In the mathematical sense, SSH does produce an array of differentially expressed sequences. This sort of "all or none" expression data provides a compliment to array hybridization methods since the normalization step means that SSH may even detect low abundance, but differentially expressed, sequences. These genes can then be quantified by real time PCR or used to construct expression arrays [3]. Like SAGE or bend sequencing, SSH is unbiased; however, SSH requires extensive sequencing to identify the subtracted clones.

Proteomic and Genomic Analysis of Cardiovascular Disease. Edited by Jennifer E. van Eyk, Michael J. Dunn

Copyright © 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 3-527-30596-3

Fig. 8.1 Alternate views of 2-color array data. A) A traditional display of DNA array data -data presented as a false color image overlay of the Cy3 and Cy5 data channels. B) Both the top and bottom blocks show an expanded view of the same region of A. The difference between the two figures is the result of manipulation of the color mapping functions -e.g. determining what level of green or red is displayed for a given signal intensity in the Cy3 and Cy5 channels. Note that it is possible to present the reader with

Fig. 8.1 Alternate views of 2-color array data. A) A traditional display of DNA array data -data presented as a false color image overlay of the Cy3 and Cy5 data channels. B) Both the top and bottom blocks show an expanded view of the same region of A. The difference between the two figures is the result of manipulation of the color mapping functions -e.g. determining what level of green or red is displayed for a given signal intensity in the Cy3 and Cy5 channels. Note that it is possible to present the reader with dramatically different views of the data simply by manipulation of the color mapping functions. C) A linear display of array data. The top graph displays the intensity (proportional to expression level) while the bottom graph displays the Cy3/Cy5 ratio for each spot shown in B. The ordered pairs of (intensity, ratio) data contain similar information content to that in either view in B. However, the representation of the data as ordered (intensity, ratio) pairs provides a less subjective view than a false color image.

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