GeneExplorer is a web application written by Christian Rees that allows the exploration of large bodies of gene expression data generated by DNA microarray experiments using a web browser as its interface. Gene Explorer is based on the Windows program TreeView written by Michael Eisen.

A hierarchical clustering algorithm (Eisen et al. (1998)) was used to group genes based on their similarity in the expression patters. The data are shown in a tabular format in which each row of colored boxes represents the variation in transcript levels for a given gene across all of the array experiments, and each column represents the measured transcript levels for all genes in a single sample. The variation in transcript levels for each gene is represented by a color scale, in which red indicates an increase in transcript levels, and green indicates a decrease in transcript levels, relative to the unstressed sample. The saturation of the color corresponds to the magnitude of transcript variation. A black color indicates an undetectable change in expression, while a gray box indicates missing data.

An overview of the data is shown on the left pane as a "thumbnail" image, and a blown-up view of the data is shown on the right pain in a "zoom" image. By clicking on a region of interest in the "thumbnail" view, a regional enlargement will be displayed in the "zoom" field, and the ORF and gene names will be visible. By holding the mouse over a region of interest in the zoom image, the details of the experiment or gene are displayed at the top of the page.

You can also search the data for a gene name, ORF name, or keyword. To see the genes most similar in expression to the queried gene, click on the gene's colored expression bar - the top genes most similar in expression will be displayed. The length of the orange box to the right of each gene expression color bar is proportional the Pearson correlation of that gene to the queried gene.

• Complete dataset: GeneExplorer

• Figure 1: GeneExplorer

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• Figure v: GeneExplorer

• Figure vi: GeneExplorer