MRA-FET - Revision history

Smith: /* Description */

2015-03-09T21:38:22Z

‎Description

Smith: /* Overview */

2015-01-27T21:35:01Z

‎Overview

Smith: /* Overview */

2015-01-27T21:34:44Z

‎Overview

Smith: /* Note on Marker Sets */

2015-01-27T21:31:19Z

‎Note on Marker Sets

Smith: /* Note on Marker Sets */

2014-04-24T20:04:06Z

‎Note on Marker Sets

Smith: /* Detailed Listing */

2014-04-18T21:53:47Z

‎Detailed Listing

Smith: /* MRA-FET FET Parameters tab */

2014-04-18T21:38:13Z

‎MRA-FET FET Parameters tab

Smith: /* Detailed Examples */

2014-04-18T21:35:49Z

‎Detailed Examples

Smith at 23:49, 22 January 2014

2014-01-22T23:49:25Z

Smith: /* Two FET runs */

2014-01-02T20:22:14Z

‎Two FET runs

@@ Line 9: / Line 9: @@
 ==Description==
 Two choices are available in how to apply the FET method.  For either method, a one-sided FET is used.  It evaluates the right side (enrichment).
 ===One FET run===

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 This chapter details the Fisher's Exact Test method of [[Master_Regulator_Analysis|Master Regulator Analysis]].  Please see the [[Master_Regulator_Analysis|Master Regulator Analysis]] chapter for a higher-level introduction.
-'''Special note''' - MRA-FET does not use activated marker sets.  Please see the [[MRA-FET#Note_on_Marker_Sets note]] below.
+'''Special note''' - MRA-FET does not use activated marker sets.  Please see the [[MRA-FET#Note_on_Marker_Sets | note]] below.
 =FET method details=

@@ Line 3: / Line 3: @@
 =Overview=
 This chapter details the Fisher's Exact Test method of [[Master_Regulator_Analysis|Master Regulator Analysis]].  Please see the [[Master_Regulator_Analysis|Master Regulator Analysis]] chapter for a higher-level introduction.
 =FET method details=

← Older revision		Revision as of 21:31, 27 January 2015
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	====Note on Marker Sets====		====Note on Marker Sets====
−	geWorkbench provides a mechanism to restrict some analyses to using certain sets of markers by "activating" these sets in the [[Marker_Sets\| Markers]] component. However, the MRA-FET analysis component uses named marker sets directly, and does not ~~rely on~~ activated sets.	+	geWorkbench provides a mechanism to restrict some analyses to using certain sets of markers by "activating" these sets in the [[Marker_Sets\| Markers]] component. However, the MRA-FET analysis component uses named marker sets directly, and does not support use of activated marker sets.
−
−	~~'''No marker sets should be activated during MRA-FET runs as unexpected results will occur'''. (This is a known issue and is being fixed).~~

		+	As of geWorkbench 2.6.0, MRA-FET will warn the user if a marker set is activated, and will not run the analysis. In prior versions, please do not run MRA-FET with activated marker sets, as unexpected results may occur.

@@ Line 242: / Line 242: @@
 ====Note on Marker Sets====
-geWorkbench provides a mechanism to restrict some analyses to using certain sets of markers by "activating" these sets in the Markers component.  However, as the MRA analysis component uses named marker sets directly, it does not respect the activation state of marker sets in the Markers component, and such activated sets will have no effect on the analysis.
+geWorkbench provides a mechanism to restrict some analyses to using certain sets of markers by "activating" these sets in the [[Marker_Sets| Markers]] component.  However, the MRA-FET analysis component uses named marker sets directly, and does not rely on activated sets.
-However, activating microarray sets would restrict the markers used in generating the "bar graph" by the MRA viewer.
+'''No marker sets should be activated during MRA-FET runs as unexpected results will occur'''. (This is a known issue and is being fixed).

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 The columns exported are:
-* Genes in intersection set
+* Markers in intersection set
 * -log10(P-value) * sign of t-value

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 * '''FET P-Value''': The enrichment score p-value below which a regulon is considered enriched in differentially expressed genes.
-==MRA-FET FET Parameters tab==
+==FET Parameters tab==
 [[Image:MRA-FET_Parameters_FET.png|{{ImageMaxWidth}}]]

@@ Line 205: / Line 205: @@
 [[Image:MRA_graph_GBM_FOSL2_v3.png|{{ImageMaxWidth}}]]
-The bar graph shown above, for FOSL2, indicates that the expression profile of FOSL2 is positively correlated with its regulon targets having postive differential expression in the "case", mesenchymal phenotype.  FOSL2 is more active in the mesenchymal than in the proneural phenotype.
+The bar graph shown above, for FOSL2, indicates that the positive regulon of FOSL2 is up-regulated in the "case" mesenchymal phenotype, whereas the negative regulon is down-regulated.  FOSL2 is activated in the "case", mesenchymal phenotype.
@@ Line 212: / Line 212: @@
 [[Image:MRA_graph_GBM_ZNF238_v3.png|{{ImageMaxWidth}}]]
+The bar graph shown above, for ZNF238, indicates that the positive regulon of ZNF238 is down-regulated in the "case" mesenchymal phenotype, whereas the negative regulon is up-regulated.  ZNF238 activity is repressed in the "case", mesenchymal phenotype.
 ====Save Image====

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 =Viewing MRA analysis results (FET Method)=
-Following the successful completion of the MRA FET computation, a result node (MRA) appears in the Project Folder area of the geWorkbench interface, under the microarray experiment node.  Hovering the cursor over the MRA result node will show the number of master regulators found.
+Following the successful completion of the MRA FET computation, a result node (MRA) appears in the [[Workspace]], under the microarray experiment node.  Hovering the cursor over the MRA result node will show the number of master regulators found.
@@ Line 87: / Line 87: @@
-'''Note''' - if no significant MRs are found, an empty result node is returned to the Project Folders component.  The MRA viewer will appear but be empty.
+'''Note''' - if no significant MRs are found, an empty result node is returned to the [[Workspace]].  The MRA viewer will appear but be empty.
 ===Summary Listing===
@@ Line 217: / Line 217: @@
 ====Save Image====
 Via a right-click menu on the bar graph, the user can save an image of the displayed bar graph to
-* the Project as an image snapshot, or
+* the [[Workspace]] as an image snapshot, or
 * directly to a file on disk.  Available formats are PNG, JPEG, TIF and BMP.
@@ Line 264: / Line 264: @@
 In the "Main" parameters tab,
-* '''Load Network''' -  load the network, either directly from a file, or choose a network that has been loaded into the Project.
+* '''Load Network''' -  load the network, either directly from a file, or choose a network that has been loaded into the [[Workspace]].
 * '''P-value''' - The p-value for the FET may be set as desired.
@@ Line 304: / Line 304: @@
 ==Results==
-Upon completion of the analysis, an MRA results node is placed in the Project Folders tree. The analysis results can be browsed using the MRA viewer and are as shown above in the MRA Results Viewer section.
+Upon completion of the analysis, an MRA results node is placed in the [[Workspace]]. The analysis results can be browsed using the MRA viewer and are as shown above in the MRA Results Viewer section.
 =References=

@@ Line 12: / Line 12: @@
 ===Two FET runs===
 ====Division of data into sets====
 The data is sliced using two different methods, each of which in turn produces two subsets.