LINCS Query - Revision history

Smith: /* fMoA Display in Cytoscape */

2015-02-10T18:11:53Z

‎fMoA Display in Cytoscape

2015-02-10T00:12:18Z

‎Other Commands

2015-02-10T00:09:08Z

‎Link Out

2015-02-10T00:08:31Z

‎Link Out

2015-01-28T02:39:50Z

‎Network

2015-01-28T01:53:19Z

‎Link Out

2015-01-28T01:52:55Z

‎Link Out

2015-01-28T01:49:39Z

‎Link Out

2015-01-28T01:49:20Z

‎fMoA Display in Cytoscape

2014-09-17T18:46:08Z

‎Network

@@ Line 229: / Line 229: @@
 ===fMoA Display in Cytoscape===
-The TFs selected above along with their regulons are shown displayed in Cytoscape.  As "Show diff. expr." was checked, the individual targets are colored by their differential expression values.
+The TFs selected above along with their regulons are shown displayed in Cytoscape.  As "Show diff. expr." was checked, the individual targets are colored by their differential expression values.  Only targets which were used in the Viper analysis, that is, those for which differential expression data was available, are depicted.
 * '''Differential Expression Color Scale''' - Colors range along a gradient from dark blue (most underexpressed) to white (no expression change) and then from white to dark red (most overexpressed).  Green indicates a matching expression value was not found.  Hub genes were manually selected and shown in yellow.

← Older revision		Revision as of 00:12, 10 February 2015
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	[[Image:LINCS_fMoA_Network_Select_Nodes.png\|{{ImageMaxWidth}}]]		[[Image:LINCS_fMoA_Network_Select_Nodes.png\|{{ImageMaxWidth}}]]
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		+	The Edge Attribute Browser will shown the interaction type for selected edges:
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		+	[[Image:LINCS_fMoA_Network_Edge_Attributes.png]]

@@ Line 250: / Line 250: @@
 [[Image:LINCS_fMoA_Network_LinkOut_Entrez.png]]
-Clicking on the Gene item will open the selected gene's Entrez Gene web page.
+Clicking on the Pubmed item will open the selected gene's Entrez Pubmed web page.
 ====Add to Set====

@@ Line 246: / Line 246: @@
 ====Link Out====
-Here, the right-click menu to link out to Entrez Gene is illustrated.
+Here, the right-click menu to link out to Entrez Pubmed is illustrated.
 [[Image:LINCS_fMoA_Network_LinkOut_Entrez.png]]

← Older revision		Revision as of 02:39, 28 January 2015
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−	[[Image:LINCS_Cytoscape_linkout_menu.png]]	+	[[Image:LINCS_Cytoscape_linkout_menu.png\|{{ImageMaxWidth}}]]

@@ Line 243: / Line 243: @@
-Right-clicking on any node brings up a series of menus by which gene information can be looked up from a number of external sources.  Here, the use of Entrez Gene is illustrated.
+Right-clicking on any node brings up a series of menus by which gene information can be looked up from a number of external sources.
 [[Image:LINCS_fMoA_Network_LinkOut_Entrez.png]]
 Clicking on the Gene item will open the selected gene's Entrez Gene web page.
 Individual or groups of genes can be selected, for example, below a set of genes connected to two different TFs is shown.  The list appears below in the Node Attribute Browser, from where, by right-clicking on the list, it can be e.g. copied or saved to a file (Export command).  The entire Cytoscape interface in geWorkbench is depicted below.
 [[Image:LINCS_fMoA_Network_Select_Nodes.png|{{ImageMaxWidth}}]]

← Older revision		Revision as of 18:46, 17 September 2014
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	In the figure depicting a query for experimental results above, 2 drugs were selected for drug 1, while drug 2 was left free. The figure below shows the results of this two-against-all query visualized as a network. The two drug 1 compounds have been manually highlighted in yellow by selecting them with the mouse. Each of the two drug 1 compounds has a resulting connection to each drug 2 compound, with the strength of the interaction (calculated synergy) represented by the thickness of the line.		In the figure depicting a query for experimental results above, 2 drugs were selected for drug 1, while drug 2 was left free. The figure below shows the results of this two-against-all query visualized as a network. The two drug 1 compounds have been manually highlighted in yellow by selecting them with the mouse. Each of the two drug 1 compounds has a resulting connection to each drug 2 compound, with the strength of the interaction (calculated synergy) represented by the thickness of the line.
		+

	[[Image:LINCS_Network_MCF7_2_vs_all.png\|{{ImageMaxWidth}}]]		[[Image:LINCS_Network_MCF7_2_vs_all.png\|{{ImageMaxWidth}}]]
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		+	Right-clicking on any drug node will bring up a menu allowing lookup of the drug in Pubchem or Drugbank.
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		+	[[Image:LINCS_Cytoscape_linkout_menu.png]]