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.
|
