User:Comics42/Immunological Genome Project (ImmGen)

The Immunological Genome Project (ImmGen) is a collaborative scientific research project that is currently building a gene-expression microarray database for all characterized immune cells in the mouse. The overarching goal of the project is to computationally reconstruct the genetic regulatory network in immune cells. All data generated as part of ImmGen are made freely and publicly available.

The ImmGen project began in 2008 as a collaboration between several immunology and computational biology laboratories across the United States. The project has several phases, and is expected to take about three years to complete. Currently, raw data from the first phase is being released as it is generated on www.ImmGen.org.

Background
A true understanding of cell differentiation in the immune system will require a general perspective on the transcripts that are present in each cell type of the adaptive and innate immune systems, and how these profiles evolve through cell differentiation or activation by immunogenic or tolerogenic ligands. This project aims to establish the roadmap of these transcriptional states.

Gene-expression microarray compendium
The first aim of ImmGen is to generate a compendium of whole-genome microarray datasets for nearly all characterized cell populations of the adaptive and innate immune systems in the mouse, at major stages of differentiation and activation. This effort is being carried out by a group of collaborating immunology research laboratories across the U.S. Each of the laboratories brings a unique expertise in a parrticular cell lineage, and all are all employing standardized procedures for cell sorting. The compendium of microarray data will include as many immunologically relevant cell types as possible, from all lymphoid organs and other tissues which are monitored by immune cells.

Bioinformatic genetic regulatory network model
Once the microarray compendium is "complete", several groups of collaborating computational biologists will use the data to reverse-engineer the genetic regulatory network in immune cells. These "meta-analyses" should reveal several levels of genetic regulation in immune cells. At the broadest level, gene to gene interactions may correlate with cell types. At a finer level, regulatory interactions may tune cellular responses and homeostasis more globally in the immune system.

Visual representation of data
Project participants from Brown University's Computer Sciences Department are also exploring novel representation modes for the ImmGen data, developing and curating the public representation.

Current Status
Current participants include the Goldrath (UCSD, San Diego), Hardy (Fox Chase, Philadelphia), Kang (U. Mass, Worcester), Lanier (UCSF, San Francisco), Mathis/Benoist (HMS, Boston), Merad and Randolph (Mount Sinai, New York), Turley (DFCI, Boston) and Wagers (Joslin, Boston) laboratories As of May 2009, Immgen has profiled approximately 160 cell populations in the mouse.

Data access
The project's status and detailed information can be seen at www.immgen.org. This site also includes a dedicated data browser, with which users can interactively explore the expression profiles for particular genes, networks of co-regulated genes, and genes that best distinguish different cell types. Raw data are available at the NCBI's Gene Expression Omnibus ([ImmGen-GEO]http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15907)