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VisiGene feature on UCSC Genome Browser links genes to images

Monday, December 12, 2005
Written by Branwyn Wagman

Image from VisiGene browser: 10.5-day mouse embryo, Gray PA et al, 2004

The UCSC Genome Browser now contains an ever-growing image library that corresponds to the genome data it houses. This new software tool, called VisiGene, was created by Jim Kent and Galt Barber of the UCSC Genome Bioinformatics Group.

VisiGene offers in situ images that allow examination of expression patterns at both the tissue and cellular levels. The browser serves as a virtual microscope that lets viewers retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection. Users can access the VisiGene Browser from the menu on the UCSC Genome Bioinformatics home page or through a link on the details pages of known genes for which a VisiGene annotation exists.

The image database may be searched by gene symbols, authors, years of publication, body parts, GenBank or UniProt accessions, organisms, Theiler stages (mice), and Nieuwkoop/Faber stages (frogs). Following a successful search, VisiGene displays a list of thumbnails of images matching the search criteria in the left hand pane of the browser.

The initial release of VisiGene includes mouse in situ images from the Jackson Labs Gene Expression Database (GED), transcription factors in mouse embryos from the Mahoney Center for Neuro-Oncology, mouse head and brain in situ images from NCBI's Gene Expression Nervous System Atlas (GENSAT) database, and frog in situ images from the National Institute for Basic Biology (NIBB) XDB project. Within a few months, the VisiGene collection will also include images from the Allen Brain Atlas.