IDEA - Revision history

Smith: /* References */

2014-04-25T19:56:51Z

‎References

2014-01-22T22:35:56Z

‎Notes

2014-01-13T21:56:54Z

‎Notes

2014-01-13T21:54:36Z

‎IDEA

2013-07-16T19:23:03Z

‎Significant Genes tab

2013-07-16T19:22:37Z

‎Analysis

2013-01-17T22:00:43Z

‎Notes

2012-11-12T20:50:19Z

‎Notes

2012-11-12T20:49:46Z

‎Notes

2012-11-12T20:49:02Z

‎Notes

← Older revision		Revision as of 19:56, 25 April 2014
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	==References==		==References==

−	Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A. (2008) A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol. (4):169. [http://www.ncbi.nlm.nih.gov/pubmed/18277385 PMID:18277385]	+	Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A. (2008) A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol. (4):169. [http://www.ncbi.nlm.nih.gov/pubmed/18277385 PMID:18277385], [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267731/ PMC2267731]

@@ Line 32: / Line 32: @@
 ==Notes==
-Networks read in from files into the geWorkbench Project Folders component can be represented as Entrez ID, gene symbol, or probeset id.  However, geWorkbench currently converts Entrez ID networks to gene symbols.
+Networks read in from files into the geWorkbench [[Workspace]] can be represented as Entrez ID, gene symbol, or probeset id.  However, geWorkbench currently converts Entrez ID networks to gene symbols.
 Genes/Probesets that have no EntrezID, e.g. have "---" for their EntrezId in the annotation file, are excluded from the network during IDEA analysis (Mantis issue #2862).
-The network can be loaded from the Project, or loaded directly from file in ADJ or SIF format.
+The network can be loaded from the [[Workspace]], or loaded directly from file in ADJ or SIF format.
 If the network contains nodes that are not found in the current microarray data set, a warning pop-up appears.

@@ Line 33: / Line 33: @@
 ==Notes==
 Networks read in from files into the geWorkbench Project Folders component can be represented as Entrez ID, gene symbol, or probeset id.  However, geWorkbench currently converts Entrez ID networks to gene symbols.
 Genes/Probesets that have no EntrezID, e.g. have "---" for their EntrezId in the annotation file, are excluded from the network during IDEA analysis (Mantis issue #2862).
@@ Line 50: / Line 48: @@
 If an error occurs during remote (grid) execution, the script will extract the error from the Matlab output file and report it back to geWorkbench.
 ==References==
 Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A. (2008) A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas.  Mol Syst Biol. (4):169. [http://www.ncbi.nlm.nih.gov/pubmed/18277385 PMID:18277385]

@@ Line 6: / Line 6: @@
 The IDEA component was added to geWorkbench with release 2.3.0.  Full documentation will be available in the near future.  See Mani et al. 2008.
-The local version of IDEA has been withdrawn from geWorkbench 2.4.0 due to problems in its implementation compared with the grid version.  We expect it to return in a subsequent release.
+IDEA is available in geWorkbench only as a restricted access [[Grid_Services |Grid Service]].
 =Analysis=

@@ Line 19: / Line 19: @@
 This tab should really be called the "All Results" tab.
-[[Image:IDEA_Significant_Genes.png]]
+[[Image:IDEA_Significant_Genes.png|{{ImageMaxWidth}}]]
 ==LOC Edges==

← Older revision		Revision as of 19:22, 16 July 2013
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−	[[Image:IDEA_Analysis.png]]	+	[[Image:IDEA_Analysis.png\|{{ImageMaxWidth}}]]
−

	=Results=		=Results=

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 The IDEA analysis, for compatibility with its grid service implementation, first converts each network node, in case it is represented a gene symbol or probeset id, to an Entrez ID.  In case multiple nodes map to the same Entrez ID, they are combined.  In the case that a probeset is annotated to more than one Entrez ID, it is expanded to multiple nodes.
-Genes/Probesets that have no EntrezID, e.g. have "---" for their EntrezId in the annotation file, are excluded from the network during IDEA analysis.
+Genes/Probesets that have no EntrezID, e.g. have "---" for their EntrezId in the annotation file, are excluded from the network during IDEA analysis (Mantis issue #2862).
 The network can be loaded from the Project, or loaded directly from file in ADJ or SIF format.