PhenCode: How to view PhenCode tracks at the Genome Browser

1. Start by clicking the Load Custom Tracks button on the PhenCode home page.
2. Choose Destination="UCSC Genome Browser" and Human Genome Assembly="hg18: March 2006" from the pull-down menus, and type the gene name you wish to view in the Browser Position box. Then select the data you want to include using the check boxes, and click the Go button.
3. If a list of links is displayed, click on the one that describes the gene you wish to view.
4. A Browser page will open, showing the mutations at your selected position range in the custom track(s) labeled "Locus Variants" and/or "Swiss-Prot Variants", depending on your data source selections. (In the list of track controls, these appear under the section "Phenotype and Disease Associations".)
5. Once at the Browser, you can use all of its regular controls to move, zoom, or configure the view as usual. The PhenCode custom tracks are genome-wide, so you can examine mutations at other loci by simply browsing to a different location.

If you go back to the PhenCode pages and make different selections, each new custom track will replace the previous version. However, unselecting a data source will not delete the corresponding track; use the Browser's "manage custom tracks" button to do this.

Another track that can be useful to view alongside the variants is the ORegAnno track, which contains literature-curated regulatory elements. This is a resident track rather than a custom one; it is not displayed by default, but is located in the "Expression and Regulation" section and can be opened by choosing "pack" in the track controls below the image. (If you have set the Browser not to show the controls below the image, you can access them by clicking the "configure" button.)