caBIG® at The Jackson Laboratory
The Jackson Laboratory is contributing to a “World Wide Web” for cancer research by participating in the National Cancer Institute's caBIG® (cancer Biomedical Informatics Grid™) initiative. caBIG links researchers, physicians and patients throughout the cancer community in a voluntary network that will speed the exchange of knowledge from bench to bedside and back.
The Laboratory has been active in caBIG since the project was launched in 2004. We participate in caBIG working groups and are currently members of the Vocabularies and Common Data Elements and Integrative Cancer Research domain workspaces. Members of caBIG working groups and workspaces identify the needs of cancer researchers and clinicians and develop solutions to ensure that software applications speak the same "language." One of these solutions is the Mouse-Human Anatomy Project, coordinated by JAX Associate Professor Dr. Martin Ringwald, which enables closer integration of human and mouse clinical and basic research data. Additionally, data from the MTB (Mouse Tumor Biology Database) is prominently featured in caMOD (Cancer Models Database), providing integration with a caBIG resource.
The Jackson Laboratory is excited to be one of the first institutions to adopt the caBIG® tool caArray 2.0, a powerful microarray data management system. caArray is accessible both through the caGrid and via a web browser graphic interface, providing a system to store and disseminate information on microarray experiments.
Microarrays are invaluable tools in biomedical research and have diverse application in many types of experiments including gene expression, array comparative genomic hybridization (aCGH), genotyping, methylation, and chromatin immunoprecipitation (ChIP). caArray represents microarray data with details about the experiment including the platform used and experimental design to enable data re-use and analysis.
We have modified our in-house MicroArray Database (MAD) to allow Laboratory researchers to continue using their familiar process to initiate experiments to determine, for example, gene expression changes or genomic aberrations in cancer. Once the experiments are completed, the researcher can easily transfer the data to caArray and make it available to other researchers worldwide.
Along with caArray 2.0, we have adopted a suite of software applications (Bioconductor, GenePattern and geWorkbench) that have been adapted for caBIG to help researchers analyze their microarray data. One of these, GenePattern, is an open-source statistical analysis tool developed by the Broad Institute. It is a scientific workflow platform with dozens of analytical modules. Statisticians and software engineers at The Jackson Laboratory are developing microarray experiment analysis modules for use in GenePattern. These modules utilize the Bioconductor package, R/maanova, which was developed at The Jackson Laboratory. The first pipeline, for analyzing Affymetrix gene expression experiments is now available for public use.