Marker Annotations - Revision history

Smith: /* Changes in geWorkbench 2.5.0 */

2014-01-22T23:27:13Z

‎Changes in geWorkbench 2.5.0

Smith: /* Pathway and Gene Annotations */

2014-01-22T23:24:23Z

‎Pathway and Gene Annotations

Smith: /* Pathway and Gene Annotations */

2014-01-22T23:23:38Z

‎Pathway and Gene Annotations

Smith: /* Pathway and Gene Annotations */

2014-01-22T23:20:47Z

‎Pathway and Gene Annotations

Smith: /* Pathway and Gene Annotations */

2014-01-22T23:17:57Z

‎Pathway and Gene Annotations

Smith: /* Submit Query */

2014-01-22T23:16:47Z

‎Submit Query

Smith: /* Changes in geWorkbench 2.5.0 */

2014-01-22T23:15:42Z

‎Changes in geWorkbench 2.5.0

Smith: /* Pathway and Gene Annotations */

2014-01-22T23:08:58Z

‎Pathway and Gene Annotations

Smith: /* Submit Query */

2014-01-22T23:01:49Z

‎Submit Query

Smith: /* References */

2013-10-23T20:16:05Z

‎References

← Older revision		Revision as of 23:27, 22 January 2014
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−
−	~~==Changes in geWorkbench 2.5.0==~~
−	~~In September 2013 the NCI dropped support for the caBIO data source, including access to the Cancer Gene Index.~~
−
−	~~geWorkbench now obtains gene annotations from the bioDBnet resource (Mudunuri et al, 2009).~~

	==Overview==		==Overview==

@@ Line 92: / Line 92: @@
 * '''Clear Diagram''' - this button clears the currently displayed diagram.
 * '''Clear History''' - this button clears the currently displayed diagram and removes all pathway history information from the pathway name drop-down box.
 ==References==

← Older revision		Revision as of 23:23, 22 January 2014
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−	A BioCarta pathway image is displayed above after selecting the "View Diagram" option from the "Annotations" tab. The drop-down box, on the top left corner above the diagram, shows the name of the currently displayed diagram. The component keeps a history of all BioCarta diagrams selected by the user; using the drop-down it is possible to switch among the corresponding pathway images. ~~The "~~Clear Diagram" button clears the currently displayed diagram. ~~The "~~Clear History" button ~~both~~ clears the currently displayed diagram and removes all pathway history information from the pathway name drop-down box.	+	A BioCarta pathway image is displayed above after selecting the "View Diagram" option from the "Annotations" tab.
		+	* '''pathway dropdown box''' - The drop-down box, on the top left corner above the diagram, shows the name of the currently displayed diagram. The component keeps a history of all BioCarta diagrams selected by the user; using the drop-down it is possible to switch among the corresponding pathway images.
		+	* '''Clear Diagram''' - this button clears the currently displayed diagram.
		+	* '''Clear History''' - this button clears the currently displayed diagram and removes all pathway history information from the pathway name drop-down box.

	==References==		==References==

@@ Line 69: / Line 69: @@
-* '''View Diagram''': available only for BioCarta pathways. Such pathways are accompanied by images offering a graphical/artistic rendition of the pathway. Selecting the "View Diagram" option will display this image within the "Pathway" tab.
+* '''View Diagram''': available only for BioCarta pathways. geWorkbench generates a diagram of the pathway based on the BioCarta description. Selecting the "View Diagram" option will display this diagram within the "Pathway" tab.
 * '''View Diagram on BioCarta site''' - View the BioCarta diagram in your browser directly on the BioCarta website.
 * '''Add pathway genes to set''': extracts the pathway genes for which there are associated probes in the microarray set currently selected by the user and places all such probes in a new marker set within the "Markers" component (by default, the marker set is named after the pathway).

← Older revision		Revision as of 23:17, 22 January 2014
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−	~~Clicking~~ on a pathway brings up a popup menu offering ~~a number~~ options:	+	Right-clicking on a pathway brings up a popup menu offering the following options:

← Older revision		Revision as of 23:16, 22 January 2014
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−	While the information is being retrieved, progress ~~indicators~~ will be shown.	+	While the information is being retrieved, a progress bar will be shown.
−
−	~~The following image is taken from a query on STAT3~~.

@@ Line 9: / Line 9: @@
 In September 2013 the NCI dropped support for the caBIO data source, including access to the Cancer Gene Index.
-geWorkbench now obtains gene annotations from the bioDBnet resource (Mudunuri et al, 2009).  The interface to the Cancer Gene Index has been removed.  The images below are in the process of being updated.
+geWorkbench now obtains gene annotations from the bioDBnet resource (Mudunuri et al, 2009).
 ==Overview==

@@ Line 49: / Line 49: @@
 The "Annotations" tab presents a summary listing of the annotations retrieved from bioDBnet:
-[[Image:Marker_Annotations_CGAP_gene.png|{{ImageMaxWidth}}]]
+[[Image:MarkerAnnotations_Results.png|{{ImageMaxWidth}}]]
-The listing contains at least one row for each gene which annotation information is available for. If a gene is associated with more than one pathways, then one row for every pathway is listed (e.g., as is the case above for CD40 and STAT3). Every row displays the marker (i.e., probeset) id, the corresponding gene name and the name of the associated pathway.
+The listing contains at least one row for each gene which annotation information is available for. If a gene is associated with more than one pathways, then one row for every pathway is listed (e.g., as is the case above for STAT3). Every row displays the marker (i.e., probeset) id, the corresponding gene name and the name of the associated pathway.
 Right-clicking on a gene name shows the following menu options.  Each will link to the named data source to display gene information in your browser:
 * '''Go to Entrez for ''gene name'''''
@@ Line 64: / Line 68: @@
-[[Image:Marker_Annotations_CGAP_pathway.png|{{ImageMaxWidth}}]]]
+[[Image:MarkerAnnotations_Pathway_Menu.png]]
 * '''View Diagram''': available only for BioCarta pathways. Such pathways are accompanied by images offering a graphical/artistic rendition of the pathway. Selecting the "View Diagram" option will display this image within the "Pathway" tab.
 * '''Add pathway genes to set''': extracts the pathway genes for which there are associated probes in the microarray set currently selected by the user and places all such probes in a new marker set within the "Markers" component (by default, the marker set is named after the pathway).
 * '''Export genes to CSV''': creates a new text file containing a listing of all pathway genes. The file format (csv = comma separated values) is compatible with Microsoft Excel.
@@ Line 82: / Line 88: @@
-[[Image:Biocarta.png]]
+[[Image:MarkerAnnotations_h_erkPathway.png]]
 A BioCarta pathway image is displayed above after selecting the "View Diagram" option from the "Annotations" tab. The drop-down box, on the top left corner above the diagram, shows the name of the currently displayed diagram. The component keeps a history of all BioCarta diagrams selected by the user; using the drop-down it is possible to switch among the corresponding pathway images. The "Clear Diagram" button clears the currently displayed diagram. The "Clear History" button both clears the currently displayed diagram and removes all pathway history information from the pathway name drop-down box.
 ==References==

@@ Line 25: / Line 25: @@
 The Marker Annotations module will retrieve information for all markers that belong to activated marker sets, or, more precisely, for the genes corresponding to those markers:
-[[Image:Select_marker_sets.png]]
+[[Image:MarkerAnnotations_Marker_set_activation.png]]
@@ Line 31: / Line 31: @@
-E.g., in the example shown above, information will be retrieved about the genes AATF, CD40, STAT3.  Clicking the "Retrieve Annotations" button initiates the communication with the NCI servers:
+E.g., in the example shown above, information will be retrieved about the genes STAT3 and CEBPB.  Clicking the "Retrieve Annotations" button initiates the communication with the remote server:
-[[Image:Data_source_checkboxes.png|{{ImageMaxWidth}}]]
+[[Image:MarkerAnnotations_Controls.png|{{ImageMaxWidth}}]]
@@ Line 43: / Line 44: @@
-[[Image:Marker_Annotations_ProgressBar_CGAP_and_CGI.png]]
+[[Image:MarkerAnnotations_ProgressBar.png]]
 ==Pathway and Gene Annotations==

← Older revision		Revision as of 20:16, 23 October 2013
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	[http://www.biocarta.com BioCarta]		[http://www.biocarta.com BioCarta]
		+
		+	[http://www.biocarta.com/legal/terms.asp Biocarta Terms of Use]