Professor Gwendolyn Randolph and Dr. Christoph Benoist (both Washington University, St. Louis, MO, USA) with their collaborators in the Immunological Genome Project (ImmGen), and in collaboration with Affymetrix, have developed a powerful data browser to help the research community chart gene expression and its regulation across the mouse immune system. Using the data browser, the team revealed a group of gene modules unique to peritoneal macrophages and predicted that these are regulated by GATA6.
The team intends for the data browser to be used by the entire research community on a regular basis. Users can provide their own input to continue to expand the database. Professor Randolph emphasizes, "ImmGen works because each participant is asking specific questions, while contributing to the whole on a scale that none of the labs could handle alone." The data browser can be used to view expression profile data of a selected gene in a group of many cell types. These expression profiles can then be correlated to modules of co-regulated genes, together with the transcription factors predicted to control them.
The ImmGen collaboration involves 15 immunology and computational biology laboratories. The objective of the collaboration is to generate comparable expression datasets for all populations and states in the mouse immune system, and to compute regulatory networks from the database. The expression data was developed using Affymetrix's arrays, and the project also relied heavily on eBioscience antibodies, which have enabled over 200 immune cell states to be represented in ImmGen.
The team believes that no other biological system has the knowledge of cell diversity, the lineage relationships, and the tools to tackle lineage variation at this level of resolution. ImmGen continues to expand the compendium to fill in missing cells and states, include other molecular species, profile challenged immune systems, and expand the regulatory connections.