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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). The interface to the Cancer Gene Index has been removed. The images below are in the process of being updated.
The Marker Annotations component enables the retrieval of biological annotation information for a collection of genes. For every gene, the following data can be retrieved:
- Links to gene detail pages.
- A set of pathways containing the gene.
All annotations are retrieved from remote servers maintained by the National Cancer Institute (NCI) bioDBnet resource of the Advanced Biomedical Computing Center (NCI Frederick).
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:
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:
While the information is being retrieved, progress indicators will be shown.
The following image is taken from a query on STAT3.
Pathway and Gene Annotations
The "Annotations" tab presents a summary listing of the annotations retrieved from bioDBnet:
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.
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
- Go to CGAP for gene name
- Go to GeneCards for gene name
Clicking on a pathway brings up a popup menu offering a number options:
- 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.
The export file contains the following columns:
- Entrez GeneId
- Entrez URL
- CGAP URL
- GeneCards URL
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.
Mudunuri,U., Che,A., Yi,M. and Stephens,R.M. (2009) bioDBnet: the biological database network. Bioinformatics, 25, 555-556. link to paper
- This page was last modified on 23 October 2013, at 20:16.
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