WormView, a Visualization Interface for C. elegans Gene Expression Data in WormBase
Vicky W. Zhou
Lincoln Stein, Sheldon McKay
Caenorhabditis elegans is a soil nematode that is one of the most studied model organisms in
biology. It is the first multi-cellular organism with a completely sequenced genome. This large
bulk of information is available in WormBase (http://www.wormbase.org), the model organism
database for C. elegans. WormBase currently contains the expression patterns for about 5,000
genes. These expression patterns were previously displayed as text, which is valuable but
difficult to digest. I enhanced the expression pattern display by creating a “coloring book”
interface, WormView, to visualize this data. I first drew a transparent base image of the worm
and 50% transparent organ overlays. I integrated these overlays with the database by using the
anatomy ontology terms for C. elegans. I then wrote a Perl script to access the anatomy ontology
terms for genes and highlight the corresponding organs in WormView. For genes with multiple
expression patterns, I added a disambiguation page that allows the user to compare patterns
quickly. The WormView image can also serve as an entry point for a new search by tissue,
instead of by gene. WormView enables users to visualize and digest data quickly, compare
expression patterns within one gene and across different genes, and search iteratively between
genes and tissues. WormView was deployed on the Gene Summary and Expression Pattern
pages on the public WormBase site in January 2007.