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Genetics, Vol. 167, 2111-2119, August 2004, Copyright © 2004
doi:10.1534/genetics.104.027532

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Genome Image Programs

Visualization and Interpretation of Escherichia coli Microarray Experiments

Daniel P. Zimmer*,1, Oleg Paliy*,2, Brian Thomas{dagger}, Prasad Gyaneshwar* and Sydney Kustu*,3

* Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
{dagger} College of Natural Resources, University of California, Berkeley, California 94720

3 Corresponding author: Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102.
E-mail: kustu{at}nature.berkeley.edu

We have developed programs to facilitate analysis of microarray data in Escherichia coli. They fall into two categories: manipulation of microarray images and identification of known biological relationships among lists of genes. A program in the first category arranges spots from glass-slide DNA microarrays according to their position in the E. coli genome and displays them compactly in genome order. The resulting genome image is presented in a web browser with an image map that allows the user to identify genes in the reordered image. Another program in the first category aligns genome images from two or more experiments. These images assist in visualizing regions of the genome with common transcriptional control. Such regions include multigene operons and clusters of operons, which are easily identified as strings of adjacent, similarly colored spots. The images are also useful for assessing the overall quality of experiments. The second category of programs includes a database and a number of tools for displaying biological information about many E. coli genes simultaneously rather than one gene at a time, which facilitates identifying relationships among them. These programs have accelerated and enhanced our interpretation of results from E. coli DNA microarray experiments. Examples are given.




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