Tutorial - GO Term Enrichment - Revision history

Smith at 21:26, 14 July 2009

2009-07-14T21:26:20Z

Smith at 23:47, 8 December 2008

2008-12-08T23:47:54Z

Smith: /* Example */

2006-08-17T01:19:13Z

‎Example

Smith at 01:17, 17 August 2006

2006-08-17T01:17:43Z

Smith: /* Example */

2006-08-17T01:13:48Z

‎Example

Smith at 01:11, 17 August 2006

2006-08-17T01:11:40Z

Smith: /* Example */

2006-08-17T01:10:05Z

‎Example

Smith: /* Example */

2006-08-17T01:04:35Z

‎Example

Smith: /* Example */

2006-08-17T01:04:14Z

‎Example

Smith at 05:20, 25 April 2006

2006-04-25T05:20:02Z

@@ Line 1: / Line 1: @@
 {{TutorialsTopNav}}
-Note - this component is not distributed as part of geWorkbench 1.6.*.
+Note - this component is not distributed as part of geWorkbench 1.6.* or latter versions.
 ==Outline==

← Older revision		Revision as of 23:47, 8 December 2008
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	{{TutorialsTopNav}}		{{TutorialsTopNav}}
		+
		+	Note - this component is not distributed as part of geWorkbench 1.6.*.

	==Outline==		==Outline==

@@ Line 11: / Line 11: @@
 ==Example==
-In this example we will use the file "webmatrix_quantile_log2_dev1.2_mv0.exp" available in the tutorial data section (coming soon).  The list of 84 markers was obtained as shown in the Hierarchical Clustering tutorial.    The marker lists can also be directly loaded from the file cluster_tree_total_pearsons_84_markers.csv  found in the tutorial data download.
+In this example we will use a set of genes originating from the file "webmatrix_quantile_log2_dev1.2_mv0.exp" available in the tutorial data section.  The list of 84 markers was obtained as shown in the Hierarchical Clustering tutorial.  The marker list can also be directly loaded from the file cluster_tree_total_pearsons_84_markers.csv  found in the tutorial data download.
 * Activate the list by checking its box in the '''Markers''' component as shown:

← Older revision		Revision as of 01:17, 17 August 2006
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	{{TutorialsTopNav}}		{{TutorialsTopNav}}
		+
		+	==Outline==
		+	In this tutorial we will
		+	#. Investigate a set of genes chosen in the Hierarchical Clustering tutorial.
		+	#. Generate a map of Gene Ontology (GO) terms matching the selected genes.
		+	#. Use the table view to find which GO categories are most significantly overrepresented.

	==Overview==		==Overview==

← Older revision		Revision as of 01:13, 17 August 2006
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	[[Image:Tutorial_GeneOntology_TableView.png]]		[[Image:Tutorial_GeneOntology_TableView.png]]
		+
		+
		+	Here we see that the category with most significant overrepresentation is "microtubule motor activity".

	Note the Save button at right on the component. This will dump the entire contents of the table to a text file with extension .dat.		Note the Save button at right on the component. This will dump the entire contents of the table to a text file with extension .dat.

← Older revision		Revision as of 01:11, 17 August 2006
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−	[[Image:Tutorial_GeneOntology_Result-~~binding~~.png]]	+	[[Image:Tutorial_GeneOntology_Result-binding2.png]]

← Older revision		Revision as of 01:10, 17 August 2006
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−	By clicking on the binding node, we can travel down to increasing levels of detail. By right-clicking on a folder icon and selecting Show Mappings->Selected List(including descendents) as shown below, we can see the gene names of the 25 genes categorized at that level.	+	By clicking on the binding node, we can travel down to increasing levels of detail. By right-clicking on a folder or file icon and selecting Show Mappings->Selected List(including descendents) as shown below, we can see the gene names of the genes categorized at or below that level, here 25 involved in ATP binding.

← Older revision		Revision as of 01:04, 17 August 2006
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−	[[Tutorial_GeneOntology_Result-binding.png]]	+	[[Image:Tutorial_GeneOntology_Result-binding.png]]

@@ Line 5: / Line 5: @@
 ==Example==
-In this example we will use the file "webmatrix_quantile_log2_dev1_mv0.exp" available in the tutorial data section (coming soon).  The lists of markers were obtained as shown in the Clustering tutorial.  The first contains 12 markers and the second 44, comprising together one larger cluster.  The marker lists can also be directly loaded from the files cluster_tree_12.csv and cluster_tree_44.csv found in the tutorial data section (coming soon).
+In this example we will use the file "webmatrix_quantile_log2_dev1.2_mv0.exp" available in the tutorial data section (coming soon).  The list of 84 markers was obtained as shown in the Hierarchical Clustering tutorial.    The marker lists can also be directly loaded from the file cluster_tree_total_pearsons_84_markers.csv  found in the tutorial data download.
-* Activate both of the lists by checking their boxes in the '''Markers''' component as shown:
+* Activate the list by checking its box in the '''Markers''' component as shown:
-* In the Gene Ontology component, choose the type of GO term that one wants, either '''Component''', '''Function''' or '''Process'''.  In this example we will select the '''Process''' tab.
+[[Image:Tutorial-Markers-ClusterTree84.png]]
 * Click on '''Map List(s)'''.
-* We see in the picture below that 33 of the 56 total markers were placed in functional categories.  By scrolling and by clicking on individual tree nodes, we can explore the tree.  We see that the largest single category, with 23 hits, was binding.
+* We see in the picture below that 49 of the 84 total genes were placed in functional categories.  By scrolling and by clicking on individual tree nodes, we can explore the tree.  We see that the largest single category, with 40 hits, was binding.
-[[Image:T_GeneOntology_TreeView.png]]
+[[Image:Tutorial_GeneOntology_Result.png]]
-By clicking on the binding node, we can travel down to  increasing levels of detail.  By right-clicking on a folder icon and selecting Show Mappings->Selected List(including descendents) as shown below, we can see the gene names of the 12 genes categorized at that level.
+By clicking on the binding node, we can travel down to  increasing levels of detail.  By right-clicking on a folder icon and selecting Show Mappings->Selected List(including descendents) as shown below, we can see the gene names of the 25 genes categorized at that level.
-[[Image:T_GeneOntology_TreeView_detail.png]]
+[[Tutorial_GeneOntology_Result-binding.png]]
@@ Line 28: / Line 30: @@
-[[Image:T_GeneOntology_TableView_function.png]]
+[[Image:Tutorial_GeneOntology_TableView.png]]
 Note the Save button at right on the component.  This will dump the entire contents of the table to a text file with extension .dat.

← Older revision		Revision as of 05:20, 25 April 2006
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	[[Image:T_GeneOntology_TreeView.png]]		[[Image:T_GeneOntology_TreeView.png]]

		+
		+	By clicking on the binding node, we can travel down to increasing levels of detail. By right-clicking on a folder icon and selecting Show Mappings->Selected List(including descendents) as shown below, we can see the gene names of the 12 genes categorized at that level.


	[[Image:T_GeneOntology_TreeView_detail.png]]		[[Image:T_GeneOntology_TreeView_detail.png]]
		+
		+
		+	A second view of the data is available by clicking on the TableView tab. This will show the degree of overrepresentation in GO categories. Here is the data for the Function category for the same list as above:
		+
		+
		+	[[Image:T_GeneOntology_TableView_function.png]]
		+
		+	Note the Save button at right on the component. This will dump the entire contents of the table to a text file with extension .dat.