caBIG™ at The Jackson Laboratory offers innovative tools to further cancer research
JAX® NOTES Issue 511, Fall 2008
Designated as a Cancer Center since 1983 by the National Cancer Institute (NCI), The Jackson Laboratory actively participates in NCI’s cancer Biomedical Information Grid (caBIG™) initiative. This initiative is a voluntary "World Wide Web" that links researchers, physicians, and patients in an effort to accelerate translational cancer research.
caBIG™ working groups and workspaces offer software solutions
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.
The Project harmonizes the Adult Mouse Anatomical Dictionary, built by the Gene Expression Database (GXD) project at JAX, and the Human Anatomical Dictionary developed by NCI. As a result, mouse and human data can be more closely integrated with clinical data pertinent to cancer and other human diseases. Another solution is caBIG™'s integration with the Mouse Tumor Biology Database (MTB), prominently featured in the Cancer Models Database.
The caArray 2.0 tool enhancesmicroarray experiments
caArray 2.0 is a new caBIG™ tool for storing and disseminating microarray experiments. It is accessible both through the caGrid and via a web browser graphic interface.
To enable researchers to reuse and analyze microarray data, caArray 2.0 includes experiment details, such as the platform used and experimental design. JAX's in-house MicroArray Database (MAD) allows its researchers to use familiar research processes and easily transfer data to caArray 2.0. Currently, 12 experimental datasets from eight Jackson Laboratory scientists are readily available, and over 50 more will be released soon.
To complement caArray 2.0, JAX has a suite of caBIG™-adapted software applications that help researchers analyze their microarray data.
These applications include the following:
- Bioconductor
- GenePattern
- geWorkbench
- Pathways Tools
To access any of these applications, go to this website.
GenePattern is an open-source statistical analysis tool developed by the Broad Institute and features dozens of analytical modules. JAX scientists are developing microarray analysis modules for GenePattern. These modules use the Bioconductor package R/maanova , developed by scientists in the laboratory of JAX Professor Gary Churchill, Ph.D.
The first data analysis pipeline for Affymetrix gene expression experiments is now available for public use. More information and instructions for downloading the pipeline are available at this website.
In short, caBIG™ is arming JAX and other cancer researchers worldwide with powerful new tools to help them coordinate their efforts to sever cancer's grip on human health!
