Difference between revisions of "Marker Sets"

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==Overview of Marker and Array Sets==
 
==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 subsets of arrays and markers for a number of purposes.
+
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.
+
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 clinical terms "Case" and "Control" to categorize these, but in a biological setting the equivalent would be "Experimental" vs "Control".
+
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 [[Array_Sets | Array_Sets]] for a discussion of the use of Array sets.
  
−
This chapter discusses the use of subsets of markers.  Please see the chapter [[Data_Subsets_-_Arrays | Data Subsets - Arrays]] for a discussion of the use of Array sets.
+
The figure below shows the Markers component located below the [[Workspace]] component in geWorkbench.  The [[Array_Sets|Arrays]] component is located in the same space, under the adjacent tab.
  
  
−
Further examples of working with sets of markers can be found in [[Tutorial_-_Differential_Expression]] and [[Tutorial_-_Clustering]].
+
[[Image:Markers_Sets_Bcell-100.png]]
  
−
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 a separate 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.
  
−
[[Image:T_Markers_basic_withProj.png]]
+
* '''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.
  
−
==Common Principles of Operation of Marker and Array Subsets==
 
  
−
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.
+
==Upper Pane Controls==
  
−
===Activating Subsets of Markers and Arrays===
+
[[Image:Markers_Upper_RightClickMenu.png]]
−
In the Markers and Arrays components, subsets of markers and arrays can be defined by the user, and also are created as the outcome of some analyses. Beside each such subset in the graphical interface is a checkbox.  Marking this box "checked" '''activates''' the subset. 
 
  
−
* '''Activating''' a subset restricts many geWorkbench components to using as input only the markers or arrays that are in such activated subsets.
+
The list in upper pane of the Markers component shows the markers loaded in the current data set.
  
−
* Marker Subsets
 
−
** If no Marker subset is active, all Markers are used.
 
−
** If at least one Marker subset is activated, affected components will only use markers in activated sets.
 
−
* Array Subsets
 
−
** If no Array subset is active, all Arrays are used.
 
−
** If at least one Array subset is activated, affected components will only use arrays in activated sets.
 
  
 +
The upper pane of the Markers component has the following controls:
 +
===Search===
 +
Search for markers by typing a portion of a gene name or descriptive term into the Search box. As each character is typed, the list is dynamically updated to contain only entries containing matches to the query so far.  The match can occur anywhere in the name or description.
  
−
==Controls==
+
For example, here "dod" has been entered, and only the two markers containing "dod" either in their gene symbol or description are displayed.
  
−
===Upper Pane===
 
  
−
[[Image:T_Markers_Upper_RightClickMenu.png]]
+
[[Image:Markers_Search_example.png]]
  
−
The list in upper pane of the Markers component shows the markers loaded in the current data set.
+
===Light Bulb icon===
 +
[[Image:T_Arrays_lightbulb.png]] - when activated [[Image:T_Markers_lightbulb_active.png]], 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.
  
−
The upper pane of the Markers component has the following controls:
 
−
* '''Search''' text field - Search for arrays by typing in a name or portion of a name. As one types, the first array 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 arrays, it will be displayed in red.
 
−
* '''Find Next''' button - find the next array matching the typed entry.
 
  
−
* [[Image:T_Arrays_lightbulb.png]] '''Light Bulb''' icon - when activated [[Image:T_Markers_lightbulb_active.png]], enables "hover text" display of marker names in this component.
+
[[Image:Marker_SelectionSet.png]]
  
 +
===Right-click menu===
 
Selecting one or more markers in the list and then right-clicking gives the following choices in a pop-up 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''' - Add the selected markers to a new or existing subset.
 
−
* '''Clear Selection''' - unhighlights the selected markers.
 
  
−
===Lower Pane===
+
====Add to Set====
 +
Selected markers can be added to a new or to an existing set.
 +
 
 +
 
 +
[[Image:Markers_AddToSet.png]]
 +
 
 +
 
 +
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.
 +
 
 +
 
 +
[[Image:T_Markers_Set_Label.png]]
 +
 
 +
 
 +
The markers are copied to the new set. Here we used the name "Custom":
 +
 
 +
 
 +
[[Image:Markers_AddToSetCustom.png]]
 +
 
 +
====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.
 +
 
 +
 
 +
[[Image:Markers_AddToSetAgain.png]]
 +
 
 +
====Clear Selection====
 +
Clear the contents of the default "Selection" marker set.
 +
 
 +
 
 +
====Sort Markers====
 +
Markers are by default displayed in the same order as the appear in the file from which they were loaded.
 +
 
 +
The list of markers can be sorted by:
 +
* '''gene name'''
 +
* '''probeset id'''
 +
* '''into the original order''' - the order of the markers as loaded from the original data file.
 +
 
 +
==Lower Pane Controls==
 +
 
 +
===Marker Sets (Context)===
 +
 
 +
[[Image:Marker_Sets_new_context.png]]
 +
 
 +
 
 +
* '''Pulldown menu''' - A list of marker set contexts.  Each context can contain different sets of markers.  All components will make use of the currently selected context.  If an analysis returns a marker set as a result, it is returned to the current marker set context.  Different contexts can be used to organize markers at different levels of detail, or different types of analyses.
 +
* '''New''' - This button will create a new, empty marker set context.
 +
 
 +
 
 +
A popup will ask for a name for the new context:
 +
 
 +
 
 +
[[Image:T_Markers_New_Marker_Set.png]]
 +
 
 +
 
 +
 
 +
The new context will appear in the menu, with only the default "Selection" set as a member.
 +
 
 +
 
 +
[[Image:Marker_Sets_New_List.png]]
 +
 
 +
===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 choices described in the following section appears:
 +
 
 +
 
 +
[[Image:Marker_Sets_Right_Click_menu.png]]
 +
 
 +
 
 +
====Rename====
 +
Rename the selected set.
 +
 
 +
====Copy====
 +
Make a copy of the selected set.
 +
 
 +
====Activate====
 +
Activate the selected set (see explanation [[Marker_Sets#Activating_Sets_of_Markers_and_Arrays | 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.
  
−
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 following choices appears:
+
[[Image:Marker_Sets_set_activated.png]]
  
−
[[Image:T_Markers_LowerRightClick_Menu.png]]
+
====Deactivate====
−
* '''Rename''' - Rename the selected subset.
+
Deactivate the selected set (see explanation [[Marker_Sets#Activating_Sets_of_Markers_and_Arrays | above]]). Deactivating a set can also be done directly by unchecking the check box before its name.
−
* '''Copy''' - Make a copy of the selected subset.
 
−
* '''Activate''' - Activate the selected subset.  This can also be done directly by checking the check box before its entry.
 
−
* '''Deactivate''' - Deactivate the selected subset.  This can also be done directly by unchecking the check box before its entry.
 
−
* '''New Set''' - Create a new empty marker subset.
 
−
* '''Delete''' - Delete the selected subset.
 
−
* '''Combine''' - Combine the selected subsets into a new subset.  Methods are:
 
−
** '''Union''' - add all arrays from all selected sets.
 
−
** '''Intersection ''' - add arrays that are in each selected set.
 
−
** '''XOR''' - add arrays that are in only one of the selected sets.
 
−
* '''Print''' - Print the selected subset of arrays.
 
−
* '''Visual Properties''' - not implemented.
 
−
* '''Save''' - not implemented.
 
−
* '''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 appear in the Cytoscape display will be highlighted yellow.
 
  
−
 
  
 +
====New Set====
 +
Create a new empty marker set.
  
 +
====Delete====
 +
Delete the selected set.
  
  
−
==Examples (Section under construction)==
+
====Combine====
 +
Combine two or more 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.
  
−
===Add a marker to the default set by double-clicking===
+
====Print====
 +
Print the names of the markers contained in the selected set(s) to a printer.
  
−
Double-clicking a marker in the upper list adds it to the default "Selection" subset.
+
====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, causes a properties editor to appear. In it, the shape and color of points representing markers in various geWorkbench graphical components can be globally altered.
  
−
[[Image:T_Marker_SelectionSet.png]]
+
[[Image:Arrays_Change_visual_properties.png]]
  
−
===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".
 
  
−
[[Image:T_Markers_AddToSet.png]]
+
The color chooser:
  
−
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.  
+
[[Image:Arrays_Change_visual_properties_choose_color.png]]
  
−
[[Image:T_Markers_Set_Label.png]]
 
  
−
The markers are copied to the new subset with name "Custom":
+
The shape chooser:
 +
 
 +
[[Image:Arrays_Change_visual_properties_choose_shape.png]]
 +
 
 +
 
 +
Chooser showing selection of a green "plus" shape to represent the marker set.
 +
 
 +
[[Image:Markers_Change_visual_properties_blue_oval.png]]
  
−
[[Image:T_Markers_AddToSetCustom.png]]
 
  
−
===Adding markers to an existing subset - shortcut===
+
After the visual properties of a marker set have been altered, we can view the markers appearance in, for example, the Scatter Plot component. 
  
−
If you wish to add new 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.
 
  
−
[[Image:T_Markers_AddToSetAgain.png]]
+
[[Image:Markers_Change_visual_properties_scatter_plot.png]]
  
−
===Subset manipulations===
+
====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.
  
−
Right-clicking on a subset brings up a menu with options described above in the lower-pane controls section.
 
  
−
[[Image:T_Markers_RightClickMenu.png]]
+
====Save====
 +
Save the chosen set of markers as a simple list (CSV format, one marker per line) to a file on disk.
  
−
Individual markers can also be selected and removed from a subset by a right-click menu.
+
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.
  
−
[[Image:T_Markers_RightClickMenu_Marker.png]]
 
  
−
===Create a new set===
+
[[Image:Marker_Sets_Save_Multiple.png]]
  
−
The New button creates a new set (group), which in turn can be used to contain a different arrangement of subsets.
+
===Removing a marker from a set===
  
−
[[Image:T_Markers_New_Marker_Set.png]]
+
One or more markers can be removed from a set by highlighting them and then right-clicking. A menu will appear with option "Remove from Set". 
  
−
Here the Set pulldown menu shows the newly created new Set.
 
  
−
[[Image:T_Marker_Sets_Avail.png]]
+
[[Image:T_Markers_RightClickMenu_Marker.png]]

Latest revision as of 14:58, 23 April 2014

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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 Array_Sets for a discussion of the use of Array sets.

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


Markers Sets Bcell-100.png

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

Markers Upper RightClickMenu.png

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 a portion of a gene name or descriptive term into the Search box. As each character is typed, the list is dynamically updated to contain only entries containing matches to the query so far. The match can occur anywhere in the name or description.

For example, here "dod" has been entered, and only the two markers containing "dod" either in their gene symbol or description are displayed.


Markers Search example.png

Light Bulb icon

T Arrays lightbulb.png - when activated T Markers lightbulb active.png, 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.


Marker SelectionSet.png

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.


Markers AddToSet.png


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.


T Markers Set Label.png


The markers are copied to the new set. Here we used the name "Custom":


Markers AddToSetCustom.png

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.


Markers AddToSetAgain.png

Clear Selection

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


Sort Markers

Markers are by default displayed in the same order as the appear in the file from which they were loaded.

The list of markers can be sorted by:

  • gene name
  • probeset id
  • into the original order - the order of the markers as loaded from the original data file.

Lower Pane Controls

Marker Sets (Context)

Marker Sets new context.png


  • Pulldown menu - A list of marker set contexts. Each context can contain different sets of markers. All components will make use of the currently selected context. If an analysis returns a marker set as a result, it is returned to the current marker set context. Different contexts can be used to organize markers at different levels of detail, or different types of analyses.
  • New - This button will create a new, empty marker set context.


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


T Markers New Marker Set.png


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


Marker Sets New List.png

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 choices described in the following section appears:


Marker Sets Right Click menu.png


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.


Marker Sets set activated.png

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 set.

Delete

Delete the selected set.


Combine

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

Arrays Change visual properties.png


The color chooser:

Arrays Change visual properties choose color.png


The shape chooser:

Arrays Change visual properties choose shape.png


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

Markers Change visual properties blue oval.png


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


Markers Change visual properties scatter plot.png

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.


Marker Sets Save Multiple.png

Removing a marker from a set

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


T Markers RightClickMenu Marker.png

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