Gala: Genome Alignment and Annotation Database

Example query 3: It is commonly recognized that many promoters contain CpG islands, and that promoters are most commonly at the 5' ends of genes. Hence regions of genomic DNA between closely spaced genes that are divergently transcribed and also contain CpG islands are particularly interesting as potential promoters.

This query relies on the use of the proximity feature to ultimately limit the amount of sequence between divergently transcribed genes to a maximum of 2 kb.

Query:

First find the main categories of interest with 3 separate queries:

Step 1 Find all the genes with a forward orientation.

Start with the query form. Under gene type select Gene, Predicted gene, and Related gene as the types of genes that will be used. For help with selecting multiple items in a selection box, click here. Under orientation select the +. Under Range select chr22. Type "+ genes" in the query description box, then click the Submit query button. (*Found 268 ranges)

Step 2 Find all the genes with a reverse orientation.

Click on Query form. Under gene type select Gene, Predicted gene, and Related gene as the types of genes that will be used. Under orientation select the -. Under Range select chr22. Type "- genes" in the query description box, then click the Submit query button. (*Found 272 ranges)

Step 3 Select all CpG islands.

Click on Query form. Under CpG islands click on the check box where it says Query all CpG islands. Under Range select chr22. Type "CpG islands" in the query description box, then click the Submit query button. (*Found 675 ranges)

Now begin to filter the dataset using various combinations of the data selected through the history page:

Step 4 Find CpG islands close to 5' end of + genes.

Click on the History page button at the top of the page. Under proximity enter the query number for the CpG islands query in the first text box. Click the radio button next to "lie within" then enter 2000 in the text box that follows the radio button. Choose upstream to only look next to the 5' end. Enter the query number for the + genes query in the last text box for proximity. Type "CpG islands 5' to + genes" in the compound query description box, then click the Submit compound query button. (*Found 269 ranges)

Step 5 Find CpG islands close to 5' end of - genes.

Enter the same as for step 4, except enter the query number for the - genes query in the last text box for proximity. Also type "CpG islands 5' to - genes" in the compound query description box. Click the Submit compound query button. (*Found 261 ranges)

Step 6 Find the CpG islands that are between oppositely transcribed genes.

Click on the History page button. Click on the checkboxes next to the queries from step 4 and 5. Click the radio button next to INTERSECTION. Type "example query 3 final results" in the compound query description box. Click the Submit compound query button. (*Found 39 ranges)

Step 7 Viewing the results.

To view the results in the Human Genome Browser one at a time, unselect the areas you are not interested in under limits. One area must be selected. Click on the View all data ... button next to a result. The data from the database for this region will be displayed. Click on the View UCSC Golden Path user track button. A new window will open with the Human Genome Browser at the location of the CpG island. Make sure the Sanger and Known genes tracks are set to full and zoom out until you can see the oppositely transcribed genes.

*NOTE: the numbers in each category and the resulting ranges may change as we continue to update our information tables.