Table 1.

Brief Instructions for Using the Controls in the PPI Viewer

Section	Control	Usage
Interaction List (see Fig. 2A)	Submit	Select the appropriate SORT KEY and its corresponding DATA TYPE, then click the Submit button.
	Go Top	Return to the top of the menu.
Interaction Network (see Fig. 2B)	ID	1. Select a clone ID, accession ID, or GI number from the upper pulldown.
Search		2. Enter any part of the letters or numbers of the ID in the entry box left to the Search button, and click the Search button.
		3. Select the gene of interest from the lower pulldown.
	KEYWORD	1. Enter a word that may be included in the annotation of the proteins, and click the Search button.
		2. Select the gene of interest from the lower pulldown.
	LUC	Choose a luciferase activity (LUC) to display the internal experimental PPIs (RIKEN_PPI) having that activity.
	CONFIDENCE	Choose a confidence to display the external public PPIs (DIP, BIND, and LITERATURE) having that confidence.
	LEVEL	Choose a level, to display proteins within the indicated number of interaction steps from the target protein.
	Reload	Click the Reload button to update the interactions display after changing any parameters.
	Go Top	Return to the top of the menu.
Assay Type List		1. If necessary, change the data source and display colors by clicking the appropriate radio buttons.
		2. Click the Reload button after making any changes.
Interaction Link	APPLET SIZE	Choose the desired applet size from the pulldown.
	View	Click to display each protein labeled with its annotation and ID number.
	Hide	Click to display each protein labeled only with its ID number.
	100-300	Choose the length of edge from the pulldown.
	Fix	Check the Fix checkbox to lock the display.