Below the Project Tree are two windows displaying information about the currently selected dataset at a glance. Project thumbnails give you a low-detail graph showing all the profiles in the dataset, as well as showing the number of profiles. To open a Gene Graph window containing the profiles displayed in the Project Thumbnail window simply left click on it.
As microarray datasets frequently are very large, you may want to show only
the mean profile of the dataset to accelerate updates of the thumbnail. To do
this click the Mean button ( 
) under the Project Thumbnail window. Click the Show all profiles button
( 
) to go back to displaying all the profiles in the dataset. Click the Groups
( 
) button in this window to toggle the use of group membership colors on or off.
By default, J-Express Pro scales the thumbnail so that all profiles can be
seen completely. To turn this off, click the Use scrollbars button (
). Scaling will be turned off, and scrollbars will be added to the Thumbview
window to allow you to see parts of the project thumbnail that extend outside
the visible area of the window. To go back to scaling the thumbnail to fit inside
the current window size, click the Fit in window button ( 
). If you’ve made changes elsewhere in J-Express Pro that are not reflected
in the Project Thumbnail window, click the Repaint button.
A project thumbnail showing a dataset containing 139 profiles.
By default, red color indicate positive values, green colors indicate negative values. In addition, intense (bright) colors indicate larger values (positive or negative) while darker colors indicate values closer to zero. For example, a dark green profile has small negative values, while a bright red profile has large positive values.
Right click on the thumbnail to set the visual properties for it. The options are :
Chart Width/Height - sets the width/height of the chart in pixels.
Color options - click any of the colored boxes to set the desired color for that option.
Paint Standard Deviation bars - check this box to include the bars indicating the standard deviation for each state.
Paint Max/Min bars - check this box to include the bars that indicate the maximum and minimum values for each state.
Include Cluster ID - check this box to display the cluster ID of a cluster on its thumbnail.
Include Cluster Size - check this box to display the amount of profiles in a cluster on its thumbnail.
Foreground Chart - check this box to display the profiles or mean profile.
Value Rectangles in Background - check this box to display the value rectangle for each of the profiles in the background of the chart. The transparency slide bar can be used to set the transparency of the foreground chart, ie. how clear the value rectangles are displayed in the back
The User Info/Meta Info window allows you to set additional information for the selected dataset and to browse the system-generated meta data.
The User Info tab provides a text area where notes can be entered without leaving J-Express Pro. These notes will be saved with the project. Note: Each dataset in a project has a separate space available for notes. Thus, you can have one set of notes describing the entire dataset, and another describing a particular subset of interest. The normal basic text editor properties are supported. Select File|Open to import a text file into the Info tab, overwriting the current content. Select File|Save to save the contents of the User Info area to a text file. To print the User Info, select File|Print. To get a preview of how the user info will look printed out, select File|Print preview. You can cut, paste, and insert text using the Edit menu. To change the look and style of the text, use the Format and Style menus. From here you can change fonts, font size, font color, and change the alignment of the text.
Each dataset in a project has its own Process List. As new datasets are added to the project tree, the Process List will be updated with the proper icon reflecting how the dataset was generated. The Process Parameters and their values of each process can be viewed by clicking on the icons in the Process List.