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.
IDEA is available in geWorkbench only as a restricted access Grid Service.
Significant Genes tab
This tab should really be called the "All Results" tab.
Loss of Correlation
Gain of Correlation
Module in Nodes
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 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.
Network conversion to Entrez IDs is carried out after the "Analyze" button is pushed.
The mutual information parameter settings are apparently fixed, no preprocessing is available.
Only genes with a NES > 0 are included in the results table.
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.
(The local IDEA analysis, not currently released, 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).
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. PMID:18277385, PMC2267731
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