3.17. "Expression profiles" dialog box

The "Expression profiles" dialog box is accessed by clicking the Analysis>Expression profiles main menu command. The dialog box displays gene expression profiles. This dialog box contains the following elements: the graph, the list of genes, the list of field groups, and the information pane (Fig. 3.17.1).

3.17.1. Graph

In the upper part of the "Expression profiles" dialog box, there are toolbar buttons that can be used to change the graphical representation of the data:

- displays the data as a histogram.
- displays the data as a graph with data markers.
- displays the data as a graph.
- displays the data as a point graph.
- displays the horizontal lines of the grid in the diagram view area.
- displays the vertical lines of the grid in the diagram view area.
- displays the diagram in pseudovolume mode (this mode is available only for bar diagrams).
- calls the "Options" dialog box.

If you click on one of experiments with your left mouse button, the gene expression profile corresponding to this experiment will be highlighted in another color in the profile view area (Fig. 3.17.1). The highlighting mode is set in the "Options" dialog box (section 3.17.6).


Figure 3.17.1 "Expression profiles" dialog box.
1. Toolbar buttons that change the view of expression profiles. 2. Marks for the groups of experiments. 3. General profile of all genes in the list. 4. Highlighted expression profile. 5. Graph. 6. List of genes. 7. List of groups. 8. Information pane.

3.17.2. Information pane

You can see the information pane below the profile view area. The information about a graph element is displayed when you point to the element with your mouse cursor (or click your mouse, depending on the settings). In the pane, you can see information about the group of experiments, which is at the current cursor position, and information about the experiment you are pointing to with your mouse cursor. The gene description is displayed below.

3.17.3. Experiments view modes

There are two view modes for experiments:

The modes are switched in the gene list.

In single-experiment mode, a profile is displayed for only one gene. The color of the elements of the expression profile depends on the color of the experimental group. Above the profile, you can see the maximum and minimum values for all groups of experiments. In the upper part of the profile view area, you can see the general profile of this gene in all experiments. The expression value is indicated on the left axis. Short names of the experiments are indicated on the horizontal axis.

In multiple-experiment mode (Fig. 3.17.1), you can see expression profiles for one and more genes. The color of the elements of the expression profiles depends on the color of the gene. Above the profile, you can see the maximum and minimum values for all genes in the list and for all groups of experiments. In the upper part of the profile view area, you can see a line marking the groups of experiments. The color of the marking line corresponds to the color of the group of experiments located above. The general profile for all genes in the list is shown above the expression profiles for separate genes.

3.17.4. Gene list

In the right upper corner of the dialog box, you can see a list of genes.

By clicking buttons at the left, you can switch between single-experiment and multiple-experiment modes. These buttons also allow you to show/hide a profile. This option (enabled/disabled) is shown by the black square located on the left side of each button.

If a button corresponding to any gene is pressed, the gene data will be displayed in single-experiment mode; otherwise, it will be displayed in multiple-experiment mode. The black square shows that this profile is displayed (); if the button has no black square in it (), this profile is hidden.

To change the color of the profile, right-click on the corresponding button. This will open a shortcut menu. Select the "Set color" command on the menu and set the color in the corresponding dialog box.

Above the list of genes, you can see buttons for quick selection/deselection of genes ( unselect, - select).

3.17.5. List of experiments

In the right lower corner of the dialog box, you can see a list of experiments. Using the buttons at the left of the names of experiments (the color of the buttons correspond to the color of the group), you can work separately with each group:

- hide the group
- show the elements selected in the list for this group. You can open the list from the shortcut menu (see below).
- display all elements in the group.

If the button for a group is pressed, this group will be displayed in single-experiment mode; otherwise, this group will be displayed in multiple-experiment mode.

Above the list of groups, you can see buttons for quickly changing the view: - hide groups, - show experiments selected in the lists of groups, - show all experiments in all groups.

Click you right mouse button to open a shortcut menu (Fig. 3.17.5.1) that has the following options:


Figure 3.17.5.1 Shortcut menu for groups.

In the list, you can select the elements to be displayed with your mouse. To select the elements to be displayed, click the box at the left of the names of the experiments: - the experiment is displayed and - the experiment is hidden. Above the list, you can see buttons for quick selection/deselection of experiments ( unselect, - select).

To confirm your selection, click "OK". The set of the elements to be displayed is valid only for displaying the experiments from the list.


Figure 3.17.5.2 "Fields list" dialog box.
1. The buttons for quick selection/deselection of experiments. 2. List of experiments. 3. The "OK" button that applies changes and closes the dialog box. 4. The "Cancel" button that closes the dialog box and cancels changes.

3.17.6. The "Options" dialog box

Selection modes:

Graph options:

Gene list options:

Group list options:

Click the "OK" button to close the dialog box and apply changes.
Click the "Apply" button to apply changes and leave the dialog box open.
Click the "Cancel" button to close the dialog box and cancel changes.


Figure 3.17.6.1 "Options" dialog box.
1. The "Selection options" pane. 2. The "Graphic options" pane. 3. The "Genes list options" pane. 4. The "Groups list options" pane. 5. The "OK" button that closes the dialog box and applies changes. 6. The "Apply" button that applies changes and leaves the dialog box open. 7. The "Cancel" button that closes the dialog box and cancels changes.