Figure 2

The FISH Oracle user interface. (1) The search menu is on the left hand side. It allows to specify a region, segment IDs, gene names and karyobands as search keys. If the user wants to display a certain genomic region, the search box is replaced by three text fields to enter the chromosome and start and end positions. A threshold for the segment mean intensity values can be specified with the "less than" or "greater than" option. Typically, the "less than" option is used with a negative threshold to focus the visualization to segments with negative mean intensity value (deletions). The "greater than" option is used with a positive threshold to focus the visualization to segments with positive mean intensity value (amplifications). The tissue type filter restricts the display to segments for one ore more specific tissue types. (2) The administration menu (lower left corner) provides functionality for data import and user account administration, e.g. activation of recently registered users. (3) Each search opens a new tab that can be identified by the search query appearing as the caption of the tab. Each open tab has its own toolbar, showing the exact location of the displayed region as well as the current thresholds. The toolbar provides buttons for zooming into the displayed region, scrolling along a chromosome, and exporting the displayed image for download to the user's computer. (4) The visualization, according to the current toolbar settings, is displayed below the toolbar. In this case, the image shows segment data and annotations in the region of the gene PTEN. (5) Clicking on the symbol representing a gene or a segment triggers a pop-up window containing corresponding detailed information.