ORIOGEN (O rder R estricted I nference for O rdered G ene E xpressio N )
and multidimensional pairwise comparisons

## ORIOGEN Main Screen

The ORIOGEN Main Screen is used to select profiles and to run the analysis. The window is divided into 4 panels as follows:

- Profile selection panel (upper left )

  This panel provides the user with radio buttons and text fields to specify profiles.

  Once the desired profile is specified, click the "Add selected profile(s)" button. The selected profile is then listed in the text panel located in the upper right.

- Text panel (upper right)

  This panel displays a summary of the user inputs, the profiles selected, and during gene processing any genes that are selected.

- Graph panel (lower left)

  This panel displays a line graph of the user selected profile based on input values.

- Button panel (lower right)

  This panel displays various buttons to modify the initial inputs, reset all selected profiles, and to start the processing of selected profiles.

  These buttons are as follows:

  - Modify initial inputs: the initial input window is re-displayed to allow changing the input values.
  - Reset all selected profiles: resets all selected profiles and clears them from the text panel.
  - Start processing: begins processing of genes, displays progress window, and indicates when processing is completed.
  - Help: displays this help screen.

In addition to the above, the following menu items are available:

- File - View Results is used to view results for the currently selected output file.
- Help - About explains the algorithm used by ORIOGEN in detail.
- Help - Contents provides a shortcut to the four main help screens.

### ORIOGEN Typical Session

A typical session would consist of the following steps:

1. Select one or more profiles by entering the appropriate information in the Profile Selection Panel. Note the Graph panel updates on the fly as profile options are selected.
2. Click the "Add Selected Profile(s)" button as each profile selection is made.
3. Review your selections in the Text Panel at the top right of the screen.
4. Click the "Start Processing" button to start running the gene selection algorithm.
5. While the gene selection processing is going on, you can click the "Stop Processing" button to pause or stop the process. If you wish to view the results so far and then continue processing, you can click the Stop button, view the results, and then click on the Continue Processing option in the Continue menu.
6. When the processing is complete, click "Yes" to view the results in graphical form. You can also click on the "Modify Initial Inputs" button, select a new input and output file name, and run another analysis.