Genome Viewer Definition | ||||
The Genome Viewer Tool shows genome-wide chromosome locations of data objects such as genes, QTLs and relevant chromosomal segments from congenic strains related to the query term. The Genome Viewer is also called the “GViewer”
[ back to top ] |
||||
What is the Genome Viewer | ||||
The GViewer provides users with a complete genome view of genes, QTLs and strains annotated to a function, biological process, cellular component, phenotype, disease or pathway term. The tool will also search for matching terms from the Gene Ontology, Mammalian Phenotype Ontology, Disease Ontology or Pathway Ontology.
[ back to top ] |
||||
To use the ontology search and its embedded GViewer to find the genes, QTLs and congenic strains annotated to a particular disease (e.g. hypertension), click the ‘Function’ panel on the home page, left center. Alternatively, you can use the stand-alone GViewer to search for multiple terms across multiple ontologies. Click here for more information about using the stand-alone GViewer.
[ back to top ] |
||||
How to use the GViewer | ||||
1. In the ‘Ontology General Search’ page that comes up, enter ‘hypertension’ in the search box in the upper center of the page. Click ‘Search’ to the right of the search box or press ‘Enter’ on your keyboard. | ||||
2. This will return an ontology term results list. To access the disease terms, click ‘CTD: Disease Ontology’. | ||||
3. Then click ‘hypertension’ in the returned term results list. Alternatively, a simpler version of the GViewer can be accessed in the ‘Genome Tools’ section from the home page. | ||||
4. The GViewer image shows all the chromosomes that have a gene (brown), QTL (blue), or congenic strain (green) annotated to the term hypertension or its children terms.
5. Clicking on the center of chromosome 3, for example, provides a more detailed image in a zoom pane. 6. Mousing over the gene marker or symbol for Cd82 in the zoom pane brings up a GBrowse gene model of that gene (red outline). Scrolling the zoom pane by dragging the highlighted (grey) slider on the chromosome or by using the zoom pane’s horizontal scroll bar at the bottom of the zoom pane allows one to see all the targeted genes and QTLs on chromosome 3 in more detail. The zoom pane shows all objects by symbol (on the left side of QTL and strain bars) and color code (brown – gene, blue-QTL, and green-strain). 7. For further analysis the mapped data can be downloaded into a spreadsheet by clicking the “CVS export” link at the bottom of the GViewer image. Clicking on the gene symbol ‘Cd82’ brings up the gene report (see Gene Report Page Help), which opens in a new window. |
||||
8. Click on ‘Send to GBrowse’ to view the region of the zoom pane in the genome browser (see Rat Genome Browser in Tools section of Help pages). Click here for more help on GViewer. |
Genome Viewer Help
|