Mouse Tumor Biology Database (MTB) Adds New Features

JAX® NOTES Issue 514, Summer 2009

Looking for cancer genes? Well, Mouse Genome Informatics has recently implemented several new features that will make your search for cancer genes in the Mouse Tumor Biology Database (MTB) more productive.

Cytogenetic Assay Image Data

The MTB now includes cytogenetic assay image data, such as images from spectral karyotyping (SKY) (Fig. 1), comparative genome hybridization (CGH), and fluorescence in situ hybridization (FISH) assays of mouse tumors. You may limit your genetics searches to cytogenetic data associated with those images. You may also link to image data from the Genetics section of the Tumor Frequency Details pages.

A New Cancer QTL Viewer

A new Cancer QTL Viewer allows you to see either all mouse cancer Quantitative Trait Loci (QTL) or only those associated with particular organs. You can see details of a particular chromosome or QTL, find candidate genes in regions of interest, and link to related data at MGI or the University of California Santa Cruz (UCSC) Genome Browser (Fig. 2). Cancer QTL data are grouped by organ, and you can select more than one organ to view cancer QTL. QTL can be viewed as html, tab delimited text, or graphically on the mouse genome (Fig. 3).

Figure 1. A SKY image from a thymus leukocyte lymphoma showing chromosome translocations.

Figure 2. QTL details link to the UCSC genome browser, allowing you to refine your search in MGI for genes that fall within QTL genome coordinates.

Figure 3. The Cancer QTL Viewer displaying a graphical view of skin cancer QTL. QTL are color coded by organ group.

Figure 4. A detail view of mouse Chromosome 5 skin cancer QTL.

Clicking on a chromosome in the graphical view increases the resolution (Fig. 4).

Please send questions and comments to User Support, mgi-help@informatics.jax.org.