geWorkbench

Overview of Marker and Array Sets

The Markers/Arrays component, located at lower left in the geWorkbench graphical interface, allows the user to define and use sets of arrays and markers for a number of purposes.

As used in geWorkbench, the term "marker" includes genes, probes/probesets, and individual sequences, depending on the type of data loaded. Sets of markers can be returned by various analysis routines. For example, the t-test returns a list of markers showing significant differential expression, and after hierarchical clustering, the markers in a subtree of the resulting dendrogram can be saved to a list.

Sets of microarrays can be used to group arrays in a meaningful fashion for statistical analysis. For example, two such phenotypes might be the diseased and normal states of a tissue from which samples have been taken. geWorkbench uses the terms "Case" and "Control" to categorize these, but in biological setting the equivalent would be "Experimental" vs "Control".

This chapter discusses the use of sets of markers. Please see the chapter Data Subsets - Arrays for a discussion of the use of Array sets.

The figure below shows the Markers component located below the Project Folders component in geWorkbench. The Arrays component is located in the same space, under the adjacent tab.

Common Principles of Operation of Marker and Array Sets

Rather than using all arrays or all markers in a data set for a particular analysis or visualization, the user may wish to restrict those used to only some subset.

Activating Sets of Markers and Arrays

In the Markers and the Arrays components, sets of markers and arrays can be defined by the user. Such sets are also created as the outcome of various analysis methods. Adjacent to each set in the graphical interface is a checkbox. Checking this box activates the subset.

• Activating a set restricts many geWorkbench components to using as input only the markers or arrays that are in one or more such activated sets.

• Marker Sets
  • If no Marker set is active, all Markers are used.
  • If at least one Marker set is activated, affected components will only use markers that are in activated sets.
• Array Sets
  • If no Array set is active, all Arrays are used.
  • If at least one Array set is activated, affected components will only use arrays that are in activated sets.

• Selection set - this is a special, default set. One is present in both the Markers component and the Arrays component. The "Selection" set has the following properties:
  • Double-clicking on a marker or array entry in the upper pane list will add that entry to the default "Selection" set. Double-clicking the same entry again will remove it from the default set.
  • The "Selection" set cannot be deleted.

Number of members displayed

The number of members in a set is given inside square brackets just to the right of the set name.

Upper Pane Controls

The list in upper pane of the Markers component shows the markers loaded in the current data set.

The upper pane of the Markers component has the following controls:

Search

Search for markers by typing in a name or portion of a name. As one types, the first marker matching the entry so far will be highlighted. In some cases however, the Find Next button must be pushed to find a match. If the typed entry matches no markers, it will be displayed in red.

Find Next

Continue search to find the next marker matching the typed entry.

Light Bulb icon

- when activated , enables "hover text" display of marker information including marker id, plus gene name and description if available (from annotation file).

Double-click action

• Double-clicking with the mouse on a marker name will add that marker to the default "Selection" set.
• Double-clicking on the same entry again will remove it from the "Selection" set.
• More generally, for any marker in the "Selection" set, double-clicking on its entry in the upper list will remove it from the set.

Right-click menu

Selecting one or more markers in the list and then right-clicking gives the following choices in a pop-up menu:

Add to Set

Selected markers can be added to a new or to an existing set.

A shortcut for adding markers to an existing set is covered in the next section.

When "Add to Set" is clicked, a dialog box will appear asking for the name of the set. Enter the name of a new or existing set.

Add to Set (Existing)

You can add markers to an existing set by either

• entering the name of the existing set in the popup dialog box, or
• before right-clicking on the selected markers, first highlight the desired marker set in the lower list. Its name will then be pre-entered into the Add to Set dialog.

Clear Selection

Clear the contents of the default "Selection" marker set.

Lower Pane Controls

The lower pane of the Markers component has the following controls:

• Marker Sets menu - Select which named set of markers to display. Each can contain a different arrangement of markers into subsets.
• New button - Create a new marker set.

If you right-click on a subset, a menu with the choices described in the following section appears:

Marker Sets pulldown menu

Select which named list of marker sets to display. Each list can contain a different arrangement of the markers into sets.

New

This button will create a new, empty list for marker sets.

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A popup will ask for a name for the new list:

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The new list will appear in the menu, with only the default "Selection" set as a member.

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Load Set

Load a list of marker ids (probeset ids) from a file on disk. The file should contain a single marker id per line. The list of marker ids will be saved to a new marker set, with the same name as the file from which it was loaded.

Load by Symbols

Load a list of gene symbols from a file on disk, with each line containing a entry. If an annotation file has been loaded which maps gene symbols to marker ids, this mapping will be used to convert the gene symbols into a standard set of marker ids. The list of marker ids will be saved to a new set, with the same name as the file from which it was loaded.

Right-click menu

If you right-click on a set, a menu with the following choices appears:

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Rename

Rename the selected set.

Copy

Make a copy of the selected set.

Activate

Activate the selected set (see explanation above). This will set the check-box in front of the set name to checked.

Activating a set can also be done directly by checking the check box before its name.

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Deactivate

Deactivate the selected set (see explanation above). Deactivating a set can also be done directly by unchecking the check box before its name.

New Set

Create a new empty marker subset.

Delete

Delete the selected set.

Combine

Combine the selected sets into a new set. Methods are:

• Union - Include all markers that appear in one or more of the selected sets.
• Intersection - Include only markers that are present in each of the selected sets.
• XOR - Include markers that are present in one and only one of the selected sets. Note that this usage differs from the logic gate XOR function.

Print

Print the names of the markers contained in the selected set(s) to a printer.

Visual Properties

Change the color and shape of points representing markers in graphical components, e.g. in the Scatter Plot.

Selecting the "Visual Properties" menu item,

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causes a properties editor to appear. In it, the shape and color of points representing arrays in various geWorkbench graphical components can be globally altered.

The color chooser:

The shape chooser:

Chooser showing selection of a green "plus" shape to represent the marker set.

After the visual properties of a marker set have been altered, we can view the markers appearance in, for example, the Scatter Plot component.

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Tag for visualization

This feature allows a set of markers to be intersected with a network displayed in the Cytoscape component. Any markers that are in the "tagged" set and which also are present in the Cytoscape network display will be highlighted yellow.

Save

Save the chosen set of markers as a simple list (CSV format, one marker per line) to a file on disk.

If more than one marker set is highlighted, two choices are offered:

• Merge into one set - The markers in all highlighted sets are merged into a single list and written out to a file. A file browser window appears that allows the user to specify the location and name of the new file.
• Save as multiple sets - Each highlighted marker set will be saved to a separate file, using the set name as the new file name. A file browser will appear which will allow the user to specify where to save the new files.

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Removing a marker from a set

One or more markers can be removed from a set by highlighting them and the right-clicking. A menu will appear with option "Remove from Set".

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Examples

Add a marker to the default set by double-clicking

Double-clicking a marker in the upper list adds it to the default "Selection" subset.

Adding markers to a new or existing subset

If one or more markers are selected in the upper list, and then right-clicked on, a menu will appear with option "Add to Set".

Choosing "Add to Set" will bring up a dialog box in which the name of a new or existing subset can be input. Here we type the name of a new marker subset "Custom" into the dialog box.

The markers are copied to the new subset with name "Custom":

Adding markers to an existing subset - shortcut

If you wish to add additional markers to an existing subset, you can avoid having to type in its name again in the dialog box by first selecting the target subset in the lower pane. Then right-click on a selection of markers above. The name of the existing subset will appear in the "Add to Set" dialog.

Manipulating marker subsets

Right-clicking on a subset brings up a menu with options described above in the lower-pane controls section.

Individual markers can also be selected and removed from a subset by a right-click menu.

Create a new set

The New button creates a new set (group), which in turn can be used to contain a different arrangement of subsets.

Here the Set pulldown menu shows the newly created new Set.