User:Daly - Revision history

Daly at 16:21, 3 April 2006

2006-04-03T16:21:36Z

Daly: /* Enrichment Analysis */

2006-02-24T20:47:32Z

‎Enrichment Analysis

Daly: /* Enrichment Analysis */

2006-02-24T20:47:09Z

‎Enrichment Analysis

Daly at 20:01, 24 February 2006

2006-02-24T20:01:00Z

Daly: /* Enrichment Analysis */

2006-02-24T19:41:31Z

‎Enrichment Analysis

Daly: /* Enrichment Analysis */

2006-02-24T19:33:08Z

‎Enrichment Analysis

Daly: /* Enrichment Analysis */

2006-02-24T19:23:18Z

‎Enrichment Analysis

Daly: /* Enrichment Analysis */

2006-02-24T19:20:27Z

‎Enrichment Analysis

Daly: /* Enrichment Analysis */

2006-02-24T19:19:22Z

‎Enrichment Analysis

Daly: /* Enrichment Analysis */

2006-02-24T19:16:15Z

‎Enrichment Analysis

@@ Line 1: / Line 1: @@
 = Overview=
+=header=
 geWorkbench is an open-source bioinformatics platform that offers a comprehensive and extendible collection of tools for the management, analysis, visualization and annotation of biomedical data.  This tool is aimed at providing researchers a centralized repository for the data analysis and visualization of gene expression data, gene sequences and protein sequences.

@@ Line 495: / Line 495: @@
-. The resulting nodes in the mapped tree will display two numbers separated by a forward slash such as '''cell(1/6058''').
+. The resulting nodes in the mapped tree will display two numbers separated by a forward slash such as '''cell (1/6058''').
 *The first number is the number of Genes mapped to a specific category and all its child nodes from the active marker panel.
 *The second numbers after the slash are the mappings as above for the reference list (or the entire chip based on the reference list check-box selection and if a reference list is loaded from the file system).

@@ Line 467: / Line 467: @@
 == Enrichment Analysis==
-In the this tutorial, you will:
+In this tutorial, you will:
 * Map markers to Gene Ontology category definitions
@@ Line 473: / Line 473: @@
-Before you can continue, geworkbench should be running. For help with this, please refer to the Getting Started (insertlink) section. The file (INSERT FILE NAME) used in the this tutorial.
+Before you can continue, geworkbench should be running. For help with this, please refer to the Getting Started (insertlink) section. The file (INSERT FILE NAME) used in this tutorial.
 '''Gene Ontology'''
-Gene Ontology component provides categorization of genes in terms of function their products perform, their cellular localization or involvement in high level biological processes. The actual category definitions are provided by the Gene Ontology Consortium (http://www.geneontology.org ) which we make use of in generating a tree structure which approximates the Directed Acyclic Graph structure used by the Consortium.  A detailed description of the Gene Ontology parameters are described in  online help.
+Gene Ontology component provides categorization of genes in terms of function their products perform, their cellular localization or involvement in high level biological processes. The actual category definitions are provided by the Gene Ontology Consortium (http://www.geneontology.org ) which we make use of in generating a tree structure which approximates the Directed Acyclic Graph structure used by the Consortium.  A detailed description of the Gene Ontology parameters is described in  online help.
@@ Line 492: / Line 492: @@
-. Click '''Map List.''' As the application creates a tree for the selected ontology,  a pop-up window will display the progress. THe mapping is based on GO mapping Annotation provided by Affymetrix in their annotation files.[[Image:E_map.png]]
+. Click '''Map List.''' As the application creates a tree for the selected ontology,  a pop-up window will display the progress. The mapping is based on GO mapping Annotation provided by Affymetrix in their annotation files.[[Image:E_map.png]]
@@ Line 503: / Line 503: @@
-The Table View and P Value Trends provides an alternate view of the mappings obtained in the Tree View.
+The Table View and P Value Trends provide an alternate view of the mappings obtained in the Tree View.

@@ Line 434: / Line 434: @@
 |-
-|1. In the Gene Panel, enter '''1973_s_at''' in the '''Find Next''' text box. The list box will navigate '''1973_s_at''', click on that gene.||[[Image: E_panel.PNG]]
+|1. In the Gene Panel, enter '''1973_s_at''' in the '''Find Next''' text box. The list box will navigate '''1973_s_at''', click on that gene.||[[Image:E_panel.png]]
 |-

← Older revision		Revision as of 19:41, 24 February 2006
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	In the this tutorial, you will:		In the this tutorial, you will:

−	* Gene Ontology	+	* Map markers to Gene Ontology category definitions

@@ Line 487: / Line 487: @@
 * AFFX-LysX-5_at
 * AFFX-LysX-3_at
 For assistance in creating a marker panel, please refer to Working with Markers and Phenotype Tutorial (INSERT LINK).

← Older revision		Revision as of 19:23, 24 February 2006
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	'''Gene Ontology'''		'''Gene Ontology'''

−	Gene Ontology component provides categorization of genes in terms of function their products perform, their cellular localization or involvement in high level biological processes. The actual category definitions are provided by the Gene Ontology Consortium (http://www.geneontology.org ) which we make use of in generating a tree structure which approximates the Directed Acyclic Graph structure used by the Consortium.	+	Gene Ontology component provides categorization of genes in terms of function their products perform, their cellular localization or involvement in high level biological processes. The actual category definitions are provided by the Gene Ontology Consortium (http://www.geneontology.org ) which we make use of in generating a tree structure which approximates the Directed Acyclic Graph structure used by the Consortium. A detailed description of the Gene Ontology parameters are described in online help.
		+

@@ Line 510: / Line 510: @@
 | [[Image:E_gotable.png]]||[[Image:E_pvalueT.png]]
 |-
-| ''' Recompute: ''' This re-computes the statistics based on the current widget settings||
+| ''' Recompute: ''' This re-computes the statistics based on the current widget settings ( pvalue metric, Min#)||
 '''Plot:''' The ‘Plot’ will draw the plot based on selections in the Tree View and widget settings in the Step Size.

@@ Line 510: / Line 510: @@
 | [[Image:E_gotable.png]]||[[Image:E_pvalueT.png]]
 |-
-| insert ||'''Slider:''' The slider on the right is a log-scaled slider that specifies a minimum P-Value for every profile to have for it to be shown in the display
+| ||
-'''Step-size:''' The ‘Step Size’ widget allows for setting the number of genes in increments to be used for the P-Value plot (the data points on the x-axis to be used). This allows for smoothing of the curve especially for very large gene list sizes.
+'''Plot:''' The ‘Plot’ will draw the plot based on selections in the Tree View and widget settings in the ‘P-Value setting’ tab.
 |--