POV (Pluggable Object Viewer) is a sophisticated database query tool. This downloadable version of POV queries a demo database where gene clusters are linked to a Gene Ontology graph (GO, http://www.geneontology.org/). LocusLink records (http://www.ncbi.nih.gov/LocusLink/) were loaded into gene clusters from the LL_tmpl flatfile.

 

To run the POV demo version, download the pov_public_app.tgz file from http://www.metagraph.org/Downloads/Downloads.html, extract the files and double-click on pov_p;ublic_app.jar. The POV Public Release Viewer window will appear (Figure 1).

 

 

 

Figure 1

 

 

Introduction to POV:

The main POV window initially is divided into two panels: a Query Panel and a Filter Panel. The Query Panel allows you to visually follow the steps of a query. The Filter Panel is used for entering information to limit searches.

 

Highlight the Gene Group item in the Query Panel. The Filter Panel now displays filters specific to Gene Group searches (in this case, information specific to the GO graph. See Figure 2.)

 

 

Figure 2

 

 

Running a Query in POV:

Suppose you’re interested in immunity. Highlight Molecular Function in the Type list, and enter “enzyme” in the Term field (Figure 3).

 

 

Figure 3

 

 

The drop down menu to the left of the Term field helps control the extent of your searches; as you can see, there are a number of ways to run text queries in POV (for example, Exact, Contains, Starts With. See Figure 4). For this search, leave the default set at Contains.

 

 

 

Figure 4

 

 

To run the query, click the Get button at the bottom-right of the Filter panel. A set of 51 Gene Group records will be returned. The set will be displayed beneath the Gene Group item in the Query Panel, and the thirteen records will be listed in a new panel in the POV window called the Result Panel (Figure 5). Click OK to return to the main window.

 

 

Figure 5

 

 

Viewing the Individual Results:

The far right panel serves two purposes. First, it is a Filter Panel used to limit searches. Second, it is an Inspector Panel that shows more details about individual search results. Highlight a record in the Result Panel (for example, enzyme modulator. You may need to adjust the Result Panel to see Terms). The detailed GO classification will be shown in the Inspector Panel (Figure 6).

 

 

Figure 6

 

 

Run Queries in Steps: Associating Gene Groups with Genes

Genes are linked to the GO graph by matching GO identifiers from LocusLink to the appropriate GO node. To find all of the genes that are linked to these 51 GO terms, highlight the Gene item in the Query Panel beneath the set of 51 Gene Groups and click the Get button at the bottom of the Filter Panel (Figure 7). Alternatively you can just double-click on the Gene item to start the query.

 

 

Figure 7

 

In this example, 4 Genes are linked to the 51 Gene Groups (Figure 8).

 

 

Figure 8

 

 

 

Viewing all of the Data:

To see which Genes correspond to what Gene Groups, update the view in the main POV window. The Result and Inspector Panels can be displayed in two modes: either side-by-side, which is the default view, or top and bottom. Switch to the top and bottom view by selecting Top and Bottom under the View menu (Figure 9).

 

 

Figure 9

 

Thus far two queries have been run. To view the associations between the results (in other words, between the 51 Gene Groups and 4 Genes), move the slider at the bottom of the Result Panel from the number 1 to 2. The slider controls the number of queries you wish to view in the Result Panel. When > 1 query is selected, the data are displayed in a table format that shows how the results from one search are related to the others (Figure 10).

 

 

Figure 10

 

 

If you are interested in a particular gene, for example arylacetamide deacetylase, highlight the corresponding record in the Result Panel to see more details about the gene in the Inspector Panel (Figure 11). For genes, the details displayed include synonyms, Locus Link information, and hyperlinks that will help you search public data sources for more information.

 

 

Figure 11