Gene Ontology Term Analysis - Revision history

Smith: /* References */

2014-04-23T19:14:19Z

‎References

Smith: /* Gene Ontology OBO file source */

2014-04-17T22:35:40Z

‎Gene Ontology OBO file source

Smith at 20:31, 22 January 2014

2014-01-22T20:31:34Z

Ut2102: /* Setup */

2013-07-16T19:07:21Z

‎Setup

Ut2102: /* Selection */

2013-07-16T19:06:34Z

‎Selection

Smith: /* Annotations */

2012-07-10T19:58:53Z

‎Annotations

Smith: /* Overview */

2012-07-10T19:49:41Z

‎Overview

Smith: /* Overview */

2012-07-10T19:49:03Z

‎Overview

Smith: /* Ontologizer */

2012-07-10T19:45:54Z

‎Ontologizer

Smith: /* Annotations */

2012-07-10T19:45:24Z

‎Annotations

← Older revision		Revision as of 19:14, 23 April 2014
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	The results of running this analysis are shown on the [[Gene_Ontology_Viewer#GO_Term_Analysis_Results \| Gene Ontology Viewer]] page.		The results of running this analysis are shown on the [[Gene_Ontology_Viewer#GO_Term_Analysis_Results \| Gene Ontology Viewer]] page.
		+
		+	=Technical Note=
		+	The "Changed Gene List" text field allows free text to be entered. However, if the parameters have been saved "Save Settings" then restoring the parameters will reload the contents of the set named in the pulldown, not the free text.

	=References=		=References=

@@ Line 22: / Line 22: @@
 =Gene Ontology OBO file source=
-By default, each time geWorkbench starts, it downloads the latest Gene Ontology OBO file from the geneontology.org website.  However, a setting in the geWorkbench [[Menu_Bar|Menu Bar]] Tools item, [[Menu_Bar#Choose_OBO_Source|"Choose OBO Source"]], allows an OBO file to be loaded locally from disk instead.
+By default, each time geWorkbench starts, it downloads the latest Gene Ontology OBO file. (The URL is now "http://purl.obolibrary.org/obo/go/go-basic.obo"). However, a setting in the geWorkbench [[Menu_Bar|Menu Bar]] Tools item, [[Menu_Bar#Choose_OBO_Source|"Choose OBO Source"]], allows an OBO file to be loaded locally from disk instead.
 [[Image:Tools_OBO_choose_source.png]]

@@ Line 53: / Line 53: @@
 * '''From Set''' - if chosen, the second pull-down shows the available sets defined in the Markers component.  The markers chosen will be converted to gene symbols without duplication.
 * '''From File''' - if chosen, the "Load" button becomes active.
-* '''From Result Node''' - if chosen, the second pull-down shows a list of available differential expression (t-test, ANOVA) result nodes from the Project Folders component.
+* '''From Result Node''' - if chosen, the second pull-down shows a list of available differential expression (t-test, ANOVA) result nodes from the [[Workspace]].
 '''Load''' - If From File is chosen, the user can load a comma-separated list of genes to use as the changed gene list.  Gene symbols must be used, not markers (probeset ids).

← Older revision		Revision as of 19:07, 16 July 2013
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−	[[Image:GeneOntology_Analysis_Setup.png]]	+	[[Image:GeneOntology_Analysis_Setup.png\|{{ImageMaxWidth}}]]

@@ Line 35: / Line 35: @@
 ===Selection===
-[[Image:GeneOntology_Analysis_Selection.png]]
+[[Image:GeneOntology_Analysis_Selection.png|{{ImageMaxWidth}}]]
 ====Reference Gene List====

@@ Line 68: / Line 68: @@
 ====Annotations====
-The annotation file links individual genes and the GO terms they are associated with.  The Ontologizer 2.0 code will automatically make use of Affymetrix 3' Expression format annotation files.  For other microarray platform types, the user will need to construct and/or provide an alternate annotation file.  As of geWorkbench release 2.2.1, annotation files obtained from  the GO Consortium (www.geneontology.org) can be loaded in addition to Affymetrix annotation files.  However, the user must ensure that the proper mapping of marker names is used between the microarray data and the annotation file.
+The annotation file links individual genes and the GO terms they are associated with.  The Ontologizer 2.0 code will automatically make use of Affymetrix 3' Expression format annotation files.  For other microarray platform types, the user will need to construct and/or provide an alternate annotation file.  As of geWorkbench release 2.2.1, annotation files obtained from  the GO Consortium (www.geneontology.org) can be loaded in addition to Affymetrix annotation files.  However, the user must ensure that the proper mapping of marker names is used between the microarray data and the annotation file.  Please see http://compbio.charite.de/contao/index.php/howto.html for further information.
 * '''Use loaded annotations''' - If an Affymetrix 3' Expression format annotation file was read in when the microarray dataset was loaded, its name is displayed here.

@@ Line 13: / Line 13: @@
-* '''Important Note on Annotation Files''' -
+* '''Important Note on Annotation Files'''
 ** The Gene Ontology Term Analysis component will automatically make use of '''Affymetrix 3' Expression''' microarray annotation data if it was loaded along with the microarray dataset.
 ** Although the Affymetrix Human Gene 1.0 ST and Human Exon 1.0 ST annotation files can be used by geWorkbench, they cannot currently be used by the ontology analysis code.

← Older revision		Revision as of 19:49, 10 July 2012
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−	* '''Important Note on Annotation Files''' - The Gene Ontology Term Analysis component will automatically make use of '''Affymetrix 3' Expression''' microarray annotation data if it was loaded along with the microarray dataset. For any other microarray platform type, the user must supply an alternate gene ontology annotation file directly in the Ontologizer setup. Annotation files obtained from the GO Consortium (www.geneontology.org) can be loaded.	+	* '''Important Note on Annotation Files''' -
		+	** The Gene Ontology Term Analysis component will automatically make use of '''Affymetrix 3' Expression''' microarray annotation data if it was loaded along with the microarray dataset.
		+	** Although the Affymetrix Human Gene 1.0 ST and Human Exon 1.0 ST annotation files can be used by geWorkbench, they cannot currently be used by the ontology analysis code.
		+	** For any other microarray platform type except the Affymetrix 3' Expression format, the user must supply an alternate gene ontology annotation file directly in the Ontologizer setup.
		+	** Annotation files obtained from the GO Consortium (www.geneontology.org) can be loaded.

	* '''Note''' - If a marker has an annotation to a GO Term but has no gene symbol, it will not be included in the "Reference Gene" list or the "Changed Gene" list.		* '''Note''' - If a marker has an annotation to a GO Term but has no gene symbol, it will not be included in the "Reference Gene" list or the "Changed Gene" list.

@@ Line 67: / Line 67: @@
 * '''Use loaded annotations''' - If an Affymetrix 3' Expression format annotation file was read in when the microarray dataset was loaded, its name is displayed here.
-* '''Use alternate annotation file''' - A new or alternate annotation file can be entered into the adjacent text field in by selecting this option.
+* '''Use alternate annotation file''' - A new or alternate annotation file can be entered into the adjacent text field in by selecting this option and choosing "Browse".
 * '''Browse''' - this button brings up a file browser for choosing an annotation file.