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.

A "bird's eye view" of the data is displayed in a "thumbnail" or "Radar" pane on the left, and a blown up view in the "Zoom" pane on the right. The "Radar" gives an overview of the gene expression data.

By clicking on a region of interest in the "Radar" view, a regional enlargement will be displayed in the "Zoom" field, and the ORF and gene names will be visible.

• Figure 4: GeneExplorer