The Mouse Tumor Biology database

Abstract

The laboratory mouse has long been an important tool in the study of the biology and genetics of human cancer. With the advent of genetic engineering techniques, DNA microarray analyses, tissue arrays and other large-scale, high-throughput data generating methods, the amount of data available for mouse models of cancer is growing exponentially. Tools to integrate, locate and visualize these data are crucial to aid researchers in their investigations. The Mouse Tumor Biology database (http://tumor.informatics.jax.org) seeks to address that need.

Figure 1. Publications for mouse models of cancer

This graph was generated from data held in PubMed. A search was performed using the terms 'mouse', 'model' and 'cancer', and the numbers of matching references for each publication year were recorded.

Figure 2. The Tumor Frequency Grid

The grid provides a visual summary of the data held in the Mouse Tumor Biology (MTB) database regarding spontaneous tumours in standard inbred strains of mice. Each cell in the grid is colour-coded based on the highest reported frequency of a tumour in each particular inbred strain. Columns and rows for substrains or organ substructures can be viewed by clicking on the associated triangles beside the strain or organ to expand the selected region of the grid (note expansion shown for substrains of the SWR strain and for substructures of the adrenal gland). All of the coloured cells that contain data are also hyperlinked. Clicking on any one of them will launch a search of the database for the records of spontaneous tumours matching the combined strain and organ criteria designated by that cell and will present these results in a ‘Tumor Results’ page. The grid is updated dynamically as data are entered into MTB.

Figure 3. Pathology Image Detail page

Each pathology image page shows a histopathological image; in this example a mammary gland fibroadenoma observed in a female FVB/N-Tg( WapTgfa)215Bri mouse. The embedded Zoomify interface allows users to change the magnification of the image and to scan the entire image at a range of image resolutions.

Figure 4. Pathology Submission Tool

Clicking on the ‘Submit Pathology Images’ link in the left-hand menu on a Mouse Tumor Biology (MTB) web page brings the user to this submission system. New users may request a log-in and password by clicking on the ‘Register for Pathology Image Submission’ link. This opens up a new e-mail that may be filled in and sent to the MTB staff. A log-in and password will then be returned by e-mail to the user. Submissions are only accessible to the originating user, and that user has control over when his/her data are ready for release to the public MTB web site. Users may enter records for one or more mice. When a set of data is ready for submission to MTB the user clicks the ‘Review and Submit Data’ button. This will notify the MTB staff that the data are ready for release. Users may also return to submitted data for future editing or addition of subsequent images. The staff may contact the submitting researcher if clarification is needed for specifics such as strain nomenclature or the genotype of the mice. Using this password-protected interface, multiple diagnoses may be entered for each mouse, and each diagnosis may be associated with multiple images.

Figure 5. The Advanced Search Form

Users can use this form to perform specific or general queries, depending on their interests. Shown in this example are the selection criteria for a search for all metastatic mammary gland adenocarcinomas that arose in transgenic mice where the strain name begins with ‘FVB’. This can be done by entering ‘FVB’ in the ‘Strain Name’ field and changing the modifier from ‘Contains’ to ‘Begins’, choosing transgenic from the ‘Strain Type’ menu, ‘Mammary gland’ from the ‘Organ/Tissue of Origin’ menu, ‘adenocarcinoma’ from the ‘Tumor Classification’ menu, and clicking the check box in the ‘Metastasis’ section.