Overview

Interaction Viewer is a Java application providing access to the DICBP database. Upon launching Interaction Viewer you will see this initial window:

o View panels: The Interaction Viewer window contains two panels, the main functionality panel at the left and the Application Log panel at the right. Each panel can be expanded or hidden by clicking the small arrows on the divider between them.

o Genes and layout: The top of the left panel shows the data source drop-down list, the gene count and interaction count for the selected data source. Shown in the middle of the left panel is the gene table which contains all the genes in the selected data source. The order for the three columns in the gene table may be rearranged by dragging and dropping the column headers. Each column in the gene table can be sorted by clicking the corresponding column header.

o Gene selection: You can select genes individually by clicking the check box for each gene in the Select column. To select all the genes in the gene table, click on the Select All button beneath the table. Likewise, clicking on the Deselect All button will deselect all the genes in the table. Clicking on the Select Rb/E2F Pathway Genes button will select only those genes involved in the Rb/E2F pathway. Clicking on the Show Selected button will write out selected gene symbols and the total number of selected genes to the Application Log panel.

o Gene interaction data: At the bottom of the left panel are four buttons; clicking on either one of the View Interactions buttons will pop up a new window showing the gene interactions involving (or among, depending on which button gets clicked) the selected genes. If no gene interactions are found for the selected genes, then there will be no pop up window - a message of "No gene interactions found!" will be written out to the Application Log panel.

o Searches and launch Cytoscape: Clicking on the Generate Symbol File button will let you create a new line delimited text file containing all the selected gene symbols at the location you choose. This file can be used to search for your selected genes in the graph generated in Cytoscape. Clicking on the Launch Cytoscape button will launch Cytoscape (with the input file shown in the Target File Path field if specified).

Example

The following example illustrates how to use the Interaction Viewer.

1. Launch Interaction Viewer, the main window will appear as shown above.

2. Select some genes of interest. In this example, we will select two genes, E2F3 and TFE3, from the default data source which is Rb/E2F Pathway. The data in the gene table is ordered by gene ID (not shown in the table) by default. In order to find a gene by symbol, we will first sort genes by symbol. To do this, click the Gene Symbol column header to allow you to change the sorting status of that column to one of three orders: ascending, descending, or unsorted. After you select these two genes, you can verify them by clicking on the Show Selected button. The selected gene symbols will be shown in the Application Log panel.

Another easy way to check the selected genes is to sort genes by their selection status: just click the Select column header and the genes will appear at the bottom (or top, depending on how many times you click the header) of the gene table.

This is especially useful if you decide to deselect some of the genes already selected, since this way there is no need to scroll up and down the gene table to find those selected genes.

3. Click on the View Interactions (involving) button. A new window will pop up and shows the gene interactions involving the two selected genes.

Note: all the columns in this table are sortable too.

4. Click on the Generate SIF button. SIF stands for Simple Interaction File. This serves as data input to Cytoscape, a bioinformatics software platform we use to visualize gene interactions. Since we did not select a target file path in the main window, a file chooser window pops up allowing you to specify one.

Also, a message "Target file has not been specified!" is written to the Application Log panel. In this example, we will write the file to C:\Temp\test.sif. So browse to the directory C:\Temp, then type test.sif in the File Name field of the file chooser window, and click the Save button. The file test.sif is created in the directory C:\Temp. You will also see a message "SIF (involving) created for the selected genes at C:\Temp\test.sif" gets written to the Application Log panel. In addition, you will see the path C:\Temp\test.sif is shown in the Target File Path field below the gene table in the main window. You can click on the "..." button to specify a new target file path for later use. If you use any file extension other than .sif for a SIF file, you will see a message "Target file name should have .sif extension!" in the Application Log panel and the file chooser will appear again to re-enter the file name.

5. Click on the Launch Cytoscape button. Now that a SIF file is created, we will launch Cytoscape using it as input. The following Cytoscape window appears:

Maximize the Cytoscape window, click the Layout menu, select yFiles -> Circular, change the visual style from default to sample3 in the top right corner, then click the Zoom out to display all of current Graph icon in the toolbar. You will see the following screen. You can explore other layouts and find out more about Cytoscape usages on its own web site: http://www.cytoscape.org/